YASARA in press
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Computational Toxicology Wijeyesakere SJ, Richardson RJ From the book Patty's Toxicology, ISBN 9780471319436 |
![]() Richardson R Neurotoxicology 2023;98 (model, docking and cover created with YASARA, no accompanying article ) |
Iron uptake pathway of Escherichia coli as an entry route for peptide nucleic acids conjugated with a siderophore mimic. Tsylents U, Burmistrz M, Wojciechowska M, Stapie J, Maj P, Trylska J. Front Microbiol. 2024 Jan 31;15:1331021. doi: 10.3389/fmicb.2024.1331021. |
Mitoxantrone and abacavir: An ALK protein-targeted in silico proposal for the treatment of non-small cell lung cancer. Faya Castillo JE, Zapata Dongo RJ, Wong Chero PA, Infante Varillas SF. PLoS One. 2024 Feb 6;19(2):e0295966. doi: 10.1371/journal.pone.0295966. |
Mimicking Nonribosomal Peptides from the Marine Actinomycete Streptomyces sp. H-KF8 Leads to Antimicrobial Peptides. Beyer LI, Schaefer AB, Undabarrena A, Mattsby-Baltzer I, Tietze D, Svensson E, Stubelius A, Wenzel M, Camara B, Tietze AA. ACS Infect Dis. 2023 Dec 19. doi: 10.1021/acsinfecdis.3c00206. Online ahead of |
Allosteric changes in protein stability and dynamics as pathogenic mechanism for calmodulin variants not affecting Ca(2+) coordinating residues. Holler CV, Petersson NM, Brohus M, Niemelae MA, Iversen ED, Overgaard MT, Iwai H, Wimmer R. Cell Calcium. 2024 Jan;117:102831. doi: 10.1016/j.ceca.2023.102831. Epub 2023 |
Spin-Label Electron Paramagnetic Resonance Spectroscopy Reveals Effects of Wastewater Filter Membrane Coated with Titanium Dioxide Nanoparticles on Bovine Serum Albumin. Sebok-Nagy K, Kota Z, Kincses A, Fazekas AF, Der A, Laszlo Z, Pali T. Molecules. 2023 Sep 22;28(19):6750. doi: 10.3390/molecules28196750. |
Sialoglycan binding triggers spike opening in a human coronavirus. Pronker MF, Creutznacher R, Drulyte I, Hulswit RJG, Li Z, van Kuppeveld FJM, Snijder J, Lang Y, Bosch BJ, Boons GJ, Frank M, de Groot RJ, Hurdiss DL. Nature. 2023 Dec;624(7990):201-206. doi: 10.1038/s41586-023-06599-z. Epub 2023 |
Synthesis and Binding Mode Predictions of Novel Siglec-7 Ligands. Frank M, Kuhfeldt E, Cramer J, Watzl C, Prescher H. J Med Chem. 2023 Oct 26;66(20):14315-14334. doi: 10.1021/acs.jmedchem.3c01349. |
YASARA Model-Interactive Molecular Modeling from Two Dimensions to Virtual Realities. Ozvoldik K, Stockner T, Krieger E. J Chem Inf Model. 2023 Oct 23;63(20):6177-6182. doi: 10.1021/acs.jcim.3c01136. |
Anti-Diabetic Activity of Glycyrrhetinic Acid Derivatives FC-114 and FC-122: Scale-Up, In Silico, In Vitro, and In Vivo Studies. Alvarez-Almazan S, Solis-Dominguez LC, Duperou-Luna P, Fuerte-Gomez T, Gonzalez-Andrade M, Aranda-Barradas ME, Palacios-Espinosa JF, Perez-Villanueva J, Matadamas-Martinez F, Miranda-Castro SP, Mercado-Marquez C, Cortes-Benitez F. Int J Mol Sci. 2023 Aug 15;24(16):12812. doi: 10.3390/ijms241612812. |
A network pharmacology approach to elucidate the anti-inflammatory effects of ellagic acid. Hoang SH, Dao H, Lam EM. J Biomol Struct Dyn. 2023 Jul 31:1-12. doi: 10.1080/07391102.2023.2240417. |
Exploring the therapeutic potential of galidesivir analogs against Zaire ebolavirus protein 24 (V24): database screening, molecular docking, drug-relevant property evaluation and molecular dynamics simulations. Hassan HA, Abdelwahab SF, Al-Khdhairawi A, Al Zrkani MK, Rehman HM, Abdel-Rahman IM, El-Sheikh AAK, Abdelhamid MM. J Biomol Struct Dyn. 2023 Jul 21:1-11. doi: 10.1080/07391102.2023.2236720. |
Substrate-derived Sortase A inhibitors: targeting an essential virulence factor of Gram-positive pathogenic bacteria. Abujubara H, Hintzen JCJ, Rahimi S, Mijakovic I, Tietze D, Tietze AA. Chem Sci. 2023 May 31;14(25):6975-6985. doi: 10.1039/d3sc01209c. eCollection |
Insight on the mechanism of hexameric Pseudin-4 against bacterial membrane-mimetic environment. Vinutha AS, Rajasekaran R. J Comput Aided Mol Des. 2023 Jun 27. doi: 10.1007/s10822-023-00516-2. Online |
Proanthocyanidin B2 derived metabolites may be ligands for bile acid receptors S1PR2, PXR and CAR: an in silico approach. Hoang SH, Tveter KM, Mezhibovsky E, Roopchand DE. J Biomol Struct Dyn. 2023 Jun 20:1-14. doi: 10.1080/07391102.2023.2224886. |
Defensin-based therapeutic peptide design in attenuating V30M TTR-induced Familial Amyloid Polyneuropathy. Chandrasekhar G, Pengyong H, Pravallika G, Hailei L, Caixia X, Rajasekaran R. 3 Biotech. 2023 Jul;13(7):227. doi: 10.1007/s13205-023-03646-4. Epub 2023 Jun |
Computer aided therapeutic tripeptide design, in alleviating the pathogenic proclivities of nocuous synuclein fibrils. Chandrasekhar G, Srinivasan E, Nandhini S, Pravallika G, Sanjay G, Rajasekaran R. J Biomol Struct Dyn. 2023 Mar 24:1-12. doi: 10.1080/07391102.2023.2194003. |
Fibroblast growth factor 5 (FGF5) and its missense mutant FGF5-H174 underlying trichomegaly: a molecular dynamics simulation investigation. Hoang SH. J Biomol Struct Dyn. 2023 Mar 11:1-11. doi: 10.1080/07391102.2023.2188953. |
In silico analysis of dietary polyphenols and their gut microbial metabolites suggest inhibition of SARS-CoV-2 infection, replication, and host inflammatory mediators. Mezhibovsky E, Hoang SH, Szeto S, Roopchand DE. J Biomol Struct Dyn. 2023 Feb 20:1-19. doi: 10.1080/07391102.2023.2180669. |
SARS-CoV-2 proteases Mpro and PLpro: Design of inhibitors with predicted high potency and low mammalian toxicity using artificial neural networks, ligand-protein docking, molecular dynamics simulations, and ADMET calculations. Tumskiy RS, Tumskaia AV, Klochkova IN, Richardson RJ. Comput Biol Med. 2023 Feb;153:106449. doi: 10.1016/j.compbiomed.2022.106449. |
Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database. Al-Khdhairawi A, Sanuri D, Akbar R, Lam SD, Sugumar S, Ibrahim N, Chieng S, Sairi F. Comput Biol Chem. 2022 Dec 5;102:107800. doi: |
Collagen-Derived Cryptides: Machine-Learning Prediction and Molecular Dynamic Interaction Against Klebsiella pneumoniae Biofilm Synthesis Precursor Al-Khdhairawi A, Mhd-Marzuki SM, Tan ZS, Shan N, Sanuri D, Akbar R, Lam SD and Sair F Malaysian Applied Biology (2022) 51(5): 59-75 |
The free fatty acid-binding pocket is a conserved hallmark in pathogenic coronavirus spike proteins from SARS-CoV to Omicron. Toelzer C, Gupta K, Yadav SKN, Hodgson L, Williamson MK, Buzas D, Borucu U, Powers K, Stenner R, Vasileiou K, Garzoni F, Fitzgerald D, Payre C, Gautam G, Lambeau G, Davidson AD, Verkade P, Frank M, Berger I, Schaffitzel C. Sci Adv. 2022 Nov 25;8(47):eadc9179. doi: 10.1126/sciadv.adc9179. Epub 2022 |
Diverse Sensory Repertoire of Paralogous Chemoreceptors Tlp2, Tlp3, and Tlp4 in Campylobacter jejuni. Taha, Elgamoudi BA, Andrianova EP, Haselhorst T, Day CJ, Hartley-Tassell LE, King RM, Najnin T, Zhulin IB, Korolik V. Microbiol Spectr. 2022 Nov 14:e0364622. doi: 10.1128/spectrum.03646-22. Online |
Structure-based virtual screening and molecular dynamics of potential inhibitors targeting sodium-bile acid co-transporter of carcinogenic liver fluke Clonorchis sinensis. Yoo WG, Dai F, Pak JH, Hong SJ, Song JH. PLoS Negl Trop Dis. 2022 Nov 9;16(11):e0010909. doi: |
Computational Development of Inhibitors of Plasmid-Borne Bacterial Dihydrofolate Reductase. Silva PJ. Antibiotics (Basel). 2022 Jun 7;11(6). pii: 779. doi: |
Leveraging intrinsic flexibility to engineer enhanced enzyme catalytic activity. Karamitros CS, Murray K, Winemiller B, Lamb C, Stone EM, D'Arcy S, Johnson KA, Georgiou G. Proc Natl Acad Sci U S A. 2022 Jun 7;119(23):e2118979119. doi: |
An Alternative Proposal for the Reaction Mechanism of Light-Dependent Protochlorophyllide Oxidoreductase Silva PJ, Cheng Q ACS Catalysis 2022 12:2589-2605 |
Conducting the RBD of SARS-CoV-2 Omicron Variant with Phytoconstituents from Euphorbia dendroides to Repudiate the Binding of Spike Glycoprotein Using Computational Molecular Search and Simulation Approach. Hassan HA, Hassan AR, Mohamed EAR, Al-Khdhairawi A, Karkashan A, Attar R, Allemailem KS, Al Abdulmonem W, Shimizu K, Abdel-Rahman IAM, Allam AE. Molecules. 2022 May 4;27(9). pii: 2929. doi: 10.3390/molecules27092929. |
Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19. Sekar PC, Srinivasan E, Chandrasekhar G, Paul DM, Sanjay G, Surya S, Kumar NSAR, Rajasekaran R. J Mol Model. 2022 Apr 24;28(5):128. doi: 10.1007/s00894-022-05117-8. |
Elucidating novel antibacterial compounds from the NPASS database against the FimH lectin domain for the treatment of urinary tract infections: an in-silico study. Al-Zrkani MK, Abdulkareem RA, Al-Fahad D, Al Shouber M, Nasr AMS, Al-Khdhairawi A. J Biomol Struct Dyn. 2022 Apr 9:1-12. doi: 10.1080/07391102.2022.2059009. |
Molecular modeling, mutational analysis and steroid specificity of the ligand binding pocket of mPRalpha (PAQR7): Shared ligand binding with AdipoR1 and its structural basis. Kelder J, Pang Y, Dong J, Schaftenaar G, Thomas P. J Steroid Biochem Mol Biol. 2022 Feb 18;219:106082. doi: |
p21-Activated Kinase 1 Promotes Breast Tumorigenesis via Phosphorylation and Activation of the Calcium/Calmodulin-Dependent Protein Kinase II. Saldivar-Ceron HI, Villamar-Cruz O, Wells CM, Oguz I, Spaggiari F, Chernoff J, Patino-Lopez G, Huerta-Yepez S, Montecillo-Aguado M, Rivera-Pazos CM, Loza-Mejia MA, Vivar-Sierra A, Briseno-Diaz P, Zentella-Dehesa A, Leon-Del-Rio A, Lopez-Saavedra A, Padierna-Mota L, Ibarra-Sanchez MJ, Esparza-Lopez J, Hernandez-Rivas R, Arias-Romero LE. Front Cell Dev Biol. 2022 Jan 17;9:759259. doi: 10.3389/fcell.2021.759259. |
Synthesis of Nucleoside-like Molecules from a Pyrolysis Product of Cellulose and Their Computational Prediction as Potential SARS-CoV-2 RNA-Dependent RNA Polymerase Inhibitors. Defant A, Dosi F, Innocenti N, Mancini I. Int J Mol Sci. 2022 Jan 4;23(1):518. doi: 10.3390/ijms23010518. |
Hydroxypropyl Cellulose for Drug Precipitation Inhibition: From the Potential of Molecular Interactions to Performance Considering Microrheology. Niederquell A, Stoyanov E, Kuentz M. Mol Pharm. 2022 Feb 7;19(2):690-703. doi: 10.1021/acs.molpharmaceut.1c00832. Epub |
Decoding Conformational Imprint of Convoluted Molecular Interactions Between Prenylflavonoids and Aggregated Amyloid-Beta42 Peptide Causing Alzheimer's Disease. Srinivasan E, Chandrasekhar G, Chandrasekar P, Anbarasu K, Vickram AS, Tayubi IA, Rajasekaran R, Karunakaran R. Front Chem. 2021 Dec 20;9:753146. doi: 10.3389/fchem.2021.753146. eCollection |
GGCX variants leading to biallelic deficiency to carboxylate GRP cause skin laxity in VKCFD1 patients. Ghosh S, Kraus K, Biswas A, Mueller J, Forin F, Singer H, Hoening K, Hornung V, Watzka M, Oldenburg J, Czogalla-Nitsche KJ. Hum Mutat. 2022 Jan;43(1):42-55. doi: 10.1002/humu.24300. Epub 2021 Dec 2. |
Molecular simulation probes the potency of resveratrol in regulating the toxic aggregation of mutant V30M TTR fibrils in Transthyretin mediated amyloidosis. Chandrasekhar G, Srinivasan E, Sekar PC, Venkataramanan S, Rajasekaran R. J Mol Graph Model. 2022 Jan;110:108055. doi: 10.1016/j.jmgm.2021.108055. Epub |
ERK5 signalling pathway is a novel target of sorafenib: Implication in EGF biology. Ortega-Muelas M, Roche O, Fernandez-Aroca DM, Encinar JA, Albandea-Rodriguez D, Arconada-Luque E, Pascual-Serra R, Munoz I, Sanchez-Perez I, Belandia B, Ruiz-Hidalgo MJ, Sanchez-Prieto R. J Cell Mol Med. 2021 Nov;25(22):10591-10603. doi: 10.1111/jcmm.16990. Epub 2021 |
pH-Dependent Structural Dynamics of Cathepsin D-Family Aspartic Peptidase of Clonorchis sinensis. Kang JM, Le HG, Na BK, Yoo WG. Pathogens. 2021 Sep 2;10(9). pii: 1128. doi: 10.3390/pathogens10091128. |
![]() Ozvoldik K, Stockner T, Rammner B, Krieger E. J Chem Inf Model. 2021 Oct 25;61(10):5293-5303. doi: 10.1021/acs.jcim.1c00743. |
Synthesis, in silico, and in vivo anti-inflammatory evaluation of 3beta-cinnamoyloxy substituted pregna-4,16-diene-6,20-diones derivatives. Sanabria-Chanaga E, Meneses-Ruiz DM, Puertas-Santamaria EF, Mancha-Melendez FM, Bratoeff E, Loza-Mejia MA, Salazar JR. J Biomol Struct Dyn. 2021 Sep 1:1-10. doi: 10.1080/07391102.2021.1969279. |
Metformin Is a Pyridoxal-5'-phosphate (PLP)-Competitive Inhibitor of SHMT2. Tramonti A, Cuyas E, Encinar JA, Pietzke M, Paone A, Verdura S, Arbusa A, Martin-Castillo B, Giardina G, Joven J, Vazquez A, Contestabile R, Cutruzzola F, Menendez JA. Cancers (Basel). 2021 Aug 9;13(16). pii: 4009. doi: 10.3390/cancers13164009. |
Indole- and Pyrazole-Glycyrrhetinic Acid Derivatives as PTP1B Inhibitors: Synthesis, In Vitro and In Silico Studies. De-la-Cruz-Martinez L, Duran-Becerra C, Gonzalez-Andrade M, Paez-Franco JC, German-Acacio JM, Espinosa-Chavez J, Torres-Valencia JM, Perez-Villanueva J, Palacios-Espinosa JF, Soria-Arteche O, Cortes-Benitez F. Molecules. 2021 Jul 20;26(14). pii: 4375. doi: 10.3390/molecules26144375. |
von Willebrand factor propeptide missense variants affect anterograde transport to Golgi resulting in ER retention. Yadegari H, Biswas A, Ahmed S, Naz A, Oldenburg J. Hum Mutat. 2021 Jun;42(6):731-744. doi: 10.1002/humu.24204. Epub 2021 May 3. |
Analysis of electrostatic coupling throughout the laboratory evolution of a designed retroaldolase. Coulther TA, Pott M, Zeymer C, Hilvert D, Ondrechen MJ. Protein Sci. 2021 Aug;30(8):1617-1627. doi: 10.1002/pro.4099. Epub 2021 May 24. |
Multidisciplinary Approaches Identify Compounds that Bind to Human ACE2 or SARS-CoV-2 Spike Protein as Candidates to Block SARS-CoV-2-ACE2 Receptor Interactions. Day CJ, Bailly B, Guillon P, Dirr L, Jen FE, Spillings BL, Mak J, von Itzstein M, Haselhorst T, Jennings MP. mBio. 2021 Mar 30;12(2). pii: e03681-20. doi: 10.1128/mBio.03681-20. |
16-Picolyl-androsterone derivative exhibits potent 17beta-HSD3 inhibitory activity, improved metabolic stability and cytotoxic effect on various cancer cells: Synthesis, homology modeling and docking studies. Cortes-Benitez F, Roy J, Perreault M, Maltais R, Poirier D. J Steroid Biochem Mol Biol. 2021 Feb 18;210:105846. doi: |
CA10 regulates neurexin heparan sulfate addition via a direct binding in the secretory pathway. Montoliu-Gaya L, Tietze D, Kaminski D, Mirgorodskaya E, Tietze AA, Sterky FH. EMBO Rep. 2021 Feb 15:e51349. doi: 10.15252/embr.202051349. [Epub ahead of print] |
Functional and Structural Characterization of Nucleic Acid Ligands That Bind to Activated Coagulation Factor XIII. Hamedani NS, Biswas A, Rudan O, Toenges R, Meyring C, Tolle F, Mayer G, Oldenburg J, Mueller J, Poetzsch B. J Clin Med. 2021 Feb 10;10(4). pii: 677. doi: 10.3390/jcm10040677. |
In Silico Study of Polyunsaturated Fatty Acids as Potential SARS-CoV-2 Spike Protein Closed Conformation Stabilizers: Epidemiological and Computational Approaches. Vivar-Sierra A, Araiza-Macias MJ, Hernandez-Contreras JP, Vergara-Castaneda A, Ramirez-Velez G, Pinto-Almazan R, Salazar JR, Loza-Mejia MA. Molecules. 2021 Jan 29;26(3):711. doi: 10.3390/molecules26030711. |
NMR-Based Structural Characterization of a Two-Disulfide-Bonded Analogue of the FXIIIa Inhibitor Tridegin: New Insights into Structure-Activity Relationships. Schmitz T, Paul George AA, Nubbemeyer B, Baeuml CA, Steinmetzer T, Ohlenschlaeger O, Biswas A, Imhof D. Int J Mol Sci. 2021 Jan 17;22(2). pii: E880. doi: 10.3390/ijms22020880. |
A Broccoli aptamer chimera yields a fluorescent K+ sensor spanning physiological concentrations. Savage JC , Shinde P , Yao Y , Davare MA , Shinde U . Chem Commun (Camb). 2021 Feb 7;57(11):1344-1347. doi: 10.1039/d0cc07042d. Epub |
Monte-Carlo method-based QSAR model to discover phytochemical urease inhibitors using SMILES and GRAPH descriptors. Chopdar KS, Dash GC, Mohapatra PK, Nayak B, Raval MK. J Biomol Struct Dyn. 2021 Jan 6:1-10. doi: 10.1080/07391102.2020.1867643. [Epub |
New insights into the mechanism of Schiff base synthesis from aromatic amines in the absence of acid catalyst or polar solvents Silva PJ PeerJ Organic Chemistry 2:e4 DOI 10.7717/peerj-ochem.4 |
Differential Effects of IGF-1R Small Molecule Tyrosine Kinase Inhibitors BMS-754807 and OSI-906 on Human Cancer Cell Lines. Fuentes-Baile M, Ventero MP, Encinar JA, Garcia-Morales P, Poveda-Deltell M, Perez-Valenciano E, Barbera VM, Gallego-Plazas J, Rodriguez-Lescure A, Martin-Nieto J, Saceda M. Cancers (Basel). 2020 Dec 11;12(12). pii: E3717. doi: 10.3390/cancers12123717. |
Bisphenol-S and Bisphenol-F alter mouse pancreatic &Beta-cell ion channel expression and activity and insulin release through an estrogen receptor ER&Beta mediated pathway. Marroqui L, Martinez-Pinna J, Castellano-Munoz M, Dos Santos RS, Medina-Gali RM, Soriano S, Quesada I, Gustafsson JA, Encinar JA, Nadal A. Chemosphere. 2021 Feb;265:129051. doi: 10.1016/j.chemosphere.2020.129051. Epub |
Investigating the pernicious effects of heparan sulfate in serum amyloid A1 protein aggregation: a structural bioinformatics approach. Chandrasekhar G, Rajasekaran R. J Biomol Struct Dyn. 2022 Mar;40(4):1776-1790. doi: |
Design, Synthesis, and Characterization of Benzimidazole Derivatives as Positron Emission Tomography Imaging Ligands for Metabotropic Glutamate Receptor 2. Yuan G, Qu X, Zheng B, Neelamegam R, Afshar S, Iyengar S, Pan C, Wang J, Kang HJ, Ondrechen MJ, Poutiainen P, El Fakhri G, Zhang Z, Brownell AL. J Med Chem. 2020 Oct 22;63(20):12060-12072. doi: 10.1021/acs.jmedchem.0c01394. |
Inhibition of Acetylcholinesterases by Stereoisomeric Organophosphorus Compounds Containing Both Thioester and p-Nitrophenyl Leaving Groups. Talley TT, Chao CK, Berkman CE, Richardson RJ, Thompson CM. Chem Res Toxicol. 2020 Sep 21;33(9):2455-2466. doi: |
An ice-binding protein from an Arctic population of American dunegrass, Leymus mollis. Sformo TL, Raymond JA. F1000Res. 2020 Jun 26;9:648. |
Quercetin metabolites from Hibiscus sabdariffa contribute to alleviate glucolipotoxicity-induced metabolic stress in vitro. Herranz-Lopez M, Olivares-Vicente M, Rodriguez Gallego E, Encinar JA, Perez-Sanchez A, Ruiz-Torres V, Joven J, Roche E, Micol V. Food Chem Toxicol. 2020 Oct;144:111606. doi: 10.1016/j.fct.2020.111606. Epub 2020 |
Molecular Insights and Functional Consequences of the Interaction of Heme with Activated Protein C. Hopp MT, Alhanafi N, Paul George AA, Hamedani NS, Biswas A, Oldenburg J, Poetzsch B, Imhof D. Antioxid Redox Signal. 2021 Jan 1;34(1):32-48. doi: 10.1089/ars.2019.7992. Epub |
Distinct 3-disulfide-bonded isomers of tridegin differentially inhibit coagulation factor XIIIa: The influence of structural stability on bioactivity. Baeuml CA, Paul George AA, Schmitz T, Sommerfeld P, Pietsch M, Podsiadlowski L, Steinmetzer T, Biswas A, Imhof D. Eur J Med Chem. 2020 Sep 1;201:112474. doi: 10.1016/j.ejmech.2020.112474. Epub |
Computational improvement of small-molecule inhibitors of Bacillus anthracis protective antigen activation through isostere-based substitutions. Silva SVRL, Silva PJ. J Biomol Struct Dyn. 2020 Jul 14:1-9. doi: 10.1080/07391102.2020.1792987. [Epub |
The Interaction of Temozolomide with Blood Components Suggests the Potential Use of Human Serum Albumin as a Biomimetic Carrier for the Drug. Rubio-Camacho M, Encinar JA, Martinez-Tome MJ, Esquembre R, Mateo CR. Biomolecules. 2020 Jul 9;10(7). pii: E1015. doi: 10.3390/biom10071015. |
Silibinin and SARS-CoV-2: Dual Targeting of Host Cytokine Storm and Virus Replication Machinery for Clinical Management of COVID-19 Patients. Bosch-Barrera J, Martin-Castillo B, Buxo M, Brunet J, Encinar JA, Menendez JA. J Clin Med. 2020 Jun 7;9(6). pii: E1770. doi: 10.3390/jcm9061770. |
All major cholesterol-dependent cytolysins use glycans as cellular receptors. Shewell LK, Day CJ, Jen FE, Haselhorst T, Atack JM, Reijneveld JF, Everest-Dass A, James DBA, Boguslawski KM, Brouwer S, Gillen CM, Luo Z, Kobe B, Nizet V, von Itzstein M, Walker MJ, Paton AW, Paton JC, Torres VJ, Jennings MP. Sci Adv. 2020 May 22;6(21):eaaz4926. doi: 10.1126/sciadv.aaz4926. eCollection |
A single mutation increases heavy chain heterodimer assembly of bispecific antibodies by inducing structural disorder in one homodimer species. Stutz C, Blein S. J Biol Chem. 2020 May 13. pii: jbc.RA119.012335. doi: 10.1074/jbc.RA119.012335. |
Potential Drugs Targeting Early Innate Immune Evasion of SARS-Coronavirus 2 via 2'-O-Methylation of Viral RNA. Encinar JA, Menendez JA. Viruses. 2020 May 10;12(5). pii: E525. doi: 10.3390/v12050525. |
The LSD1 inhibitor iadademstat (ORY-1001) targets SOX2-driven breast cancer stem cells: a potential epigenetic therapy in luminal-B and HER2-positive breast cancer subtypes. Cuyas E, Gumuzio J, Verdura S, Brunet J, Bosch-Barrera J, Martin-Castillo B, Alarcon T, Encinar JA, Martin AG, Menendez JA. Aging (Albany NY). 2020 Mar 18;12(6):4794-4814. doi: 10.18632/aging.102887. Epub |
Repurposed Drugs That Block the Gonococcus-Complement Receptor 3 Interaction Can Prevent and Cure Gonococcal Infection of Primary Human Cervical Epithelial Cells. Poole J, Day CJ, Haselhorst T, Jen FE, Torres VJ, Edwards JL, Jennings MP. mBio. 2020 Mar 3;11(2). pii: e03046-19. doi: 10.1128/mBio.03046-19. |
Metronidazole and Secnidazole Carbamates: Synthesis, Antiprotozoal Activity, and Molecular Dynamics Studies. Rocha-Garduno G, Hernandez-Martinez NA, Colin-Lozano B, Estrada-Soto S, Hernandez-Nunez E, Prieto-Martinez FD, Medina-Franco JL, Chale-Dzul JB, Moo-Puc R, Navarrete-Vazquez G. Molecules. 2020 Feb 12;25(4). pii: E793. doi: 10.3390/molecules25040793. |
Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase. Ngu L, Winters JN, Nguyen K, Ramos KE, DeLateur NA, Makowski L, Whitford PC, Ondrechen MJ, Beuning PJ. PLoS One. 2020 Feb 6;15(2):e0228487. doi: 10.1371/journal.pone.0228487. |
Identification and characterization of a novel variant in C-terminal region of Antithrombin (Ala427Thr) associated with type II AT deficiency leading to polymer formation. Bhakuni T, Sharma A, Biswas A, Bano S, Mahapatra M, Saxena R, Jairajpuri MA. J Thromb Thrombolysis. 2020 Oct;50(3):678-685. doi: 10.1007/s11239-020-02048-0. |
Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates. Lee J, Kim TI, Le HG, Yoo WG, Kang JM, Ahn SK, Myint MK, Lin K, Kim TS, Na BK. Malar J. 2020 Feb 4;19(1):60. doi: 10.1186/s12936-020-3134-y. |
Subtle sequence variations alter tripartite complex kinetics and G-quadruplex dynamics in RNA aptamer Broccoli. Savage JC , Davare MA , Shinde U . Chem Commun (Camb). 2020 Feb 28;56(17):2634-2637. doi: 10.1039/c9cc09375c. Epub |
Toxicant interactions with macromolecular targets Richardson, RJ In: "An Introduction to Interdisciplinary Toxicology: From Molecules to Man" (Pope, C.N. and Liu, J., eds.), Elsevier/Academic Press, London, 45-57 2020, ISBN 978-0-12-813602-7 |
Partial Characterization of Two Cathepsin D Family Aspartic Peptidases of Clonorchis sinensis. Kang JM, Yoo WG, Le HG, Thai TL, Hong SJ, Sohn WM, Na BK. Korean J Parasitol. 2019 Dec;57(6):671-680. doi: 10.3347/kjp.2019.57.6.671. Epub |
Resveratrol targets PD-L1 glycosylation and dimerization to enhance antitumor T-cell immunity. Verdura S, Cuyas E, Cortada E, Brunet J, Lopez-Bonet E, Martin-Castillo B, Bosch-Barrera J, Encinar JA, Menendez JA. Aging (Albany NY). 2020 Jan 4;12(1):8-34. doi: 10.18632/aging.102646. Epub 2020 |
Presence of carbohydrate binding modules in extracellular region of class C G-protein coupled receptors (C GPCR): An in silico investigation on sweet taste receptor. Kashani-Amin E, Sakhteman A, Larijani B, Ebrahim-Habibi A. J Biosci. 2019 Dec;44(6). pii: 138. |
The Potential Synergistic Modulation of AMPK by Lippia citriodora Compounds as a Target in Metabolic Disorders. Olivares-Vicente M, Sanchez-Marzo N, Encinar JA, de la Luz Cadiz-Gurrea M, Lozano-Sanchez J, Segura-Carretero A, Arraez-Roman D, Riva C, Barrajon-Catalan E, Herranz-Lopez M, Micol V. Nutrients. 2019 Dec 4;11(12). pii: E2961. doi: 10.3390/nu11122961. |
The Plasma Factor XIII Heterotetrameric Complex Structure: Unexpected Unequal Pairing within a Symmetric Complex. Singh S, Nazabal A, Kaniyappan S, Pellequer JL, Wolberg AS, Imhof D, Oldenburg J, Biswas A. Biomolecules. 2019 Nov 21;9(12). pii: E765. doi: 10.3390/biom9120765. |
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Structural and Dynamical Basis of G Protein Inhibition by YM-254890 and FR900359: An Inhibitor in Action. Tietze D, Kaufmann D, Tietze AA, Voll A, Reher R, Koenig G, Hausch F. J Chem Inf Model. 2019 Sep 26. doi: 10.1021/acs.jcim.9b00433. |
Characterization of the mutation spectrum in a Pakistani cohort of type 3 von Willebrand disease. Ahmed S, Yadegari H, Naz A, Biswas A, Budde U, Saqlain N, Amanat S, Tariq S, Raziq F, Masood S, Pavlova A, Shamsi TS, Oldenburg J. Haemophilia. 2019 Nov;25(6):1035-1044. doi: 10.1111/hae.13841. Epub 2019 Sep 18. |
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Cardiotonic steroids as potential Na+/K+-ATPase inhibitors - a computational study. Patel CN, Kumar SP, Modi KM, Soni MN, Modi NR, Pandya HA. J Recept Signal Transduct Res. 2019 Jun;39(3):226-234. doi: |
Discovery and development of substituted thiadiazoles as inhibitors of Staphylococcus aureus Sortase A. Wehrli PM, Uzelac I, Olsson T, Jacso T, Tietze D, Gottfries J. Bioorg Med Chem. 2019 Aug 7:115043. doi: 10.1016/j.bmc.2019.115043 |
Structure functional insights into calcium binding during the activation of coagulation factor XIII A. Singh S, Dodt J, Volkers P, Hethershaw E, Philippou H, Ivaskevicius V, Imhof D, Oldenburg J, Biswas A. Sci Rep. 2019 Aug 5;9(1):11324. doi: 10.1038/s41598-019-47815-z. |
Revisiting silibinin as a novobiocin-like Hsp90 C-terminal inhibitor: Computational modeling and experimental validation. Cuyas E, Verdura S, Micol V, Joven J, Bosch-Barrera J, Encinar JA, Menendez JA. Food Chem Toxicol. 2019 Oct;132:110645. doi: 10.1016/j.fct.2019.110645. Epub 2019 |
Identification of Potential Novel Interacting Partners for Coagulation Factor XIII B (FXIII-B) Subunit, a Protein Associated with a Rare Bleeding Disorder. Singh S, Akhter MS, Dodt J, Volkers P, Reuter A, Reinhart C, Krettler C, Oldenburg J, Biswas A. Int J Mol Sci. 2019 May 31;20(11). pii: E2682. doi: 10.3390/ijms20112682. |
Synthesis, biological evaluation and computational study of novel isoniazid containing 4H-Pyrimido[2,1-b]benzothiazoles derivatives. Bhoi MN, Borad MA, Jethava DJ, Acharya PT, Pithawala EA, Patel CN, Pandya HA, Patel HD. Eur J Med Chem. 2019 Sep 1;177:12-31. doi: 10.1016/j.ejmech.2019.05.028. Epub |
Introducing a New Model of Sweet Taste Receptor, a Class C G-protein Coupled Receptor (C GPCR). Kashani-Amin E, Sakhteman A, Larijani B, Ebrahim-Habibi A. Cell Biochem Biophys. 2019 May 8. doi: 10.1007/s12013-019-00872-7 |
Binding assessment of methylene blue to human serum albumin and poly(acrylic acid): Experimental and computer-aided modeling studies. Cojocaru C, Clima L J Mol Liq. Volume 285, 1 July 2019, Pages 811-821 |
A ribose modification of Spinach aptamer accelerates lead(ii) cation association in vitro. Savage JC, Shinde P, Baechinger HP, Davare MA, Shinde U. Chem Commun (Camb). 2019 May 25;55(42):5882-5885. doi: 10.1039/c9cc01697j. Epub |
The extra virgin olive oil phenolic oleacein is a dual substrate-inhibitor of catechol-O-methyltransferase. Cuyas E, Verdura S, Lozano-Sanchez J, Viciano I, Llorach-Pares L, Nonell-Canals A, Bosch-Barrera J, Brunet J, Segura-Carretero A, Sanchez-Martinez M, Encinar JA, Menendez JA. Food Chem Toxicol. 2019 Mar 29;128:35-45. doi: 10.1016/j.fct.2019.03.049 |
Exploring the structural similarity yet functional distinction between coagulation factor XIII-B and complement factor H sushi domains. Akhter MS, Singh S, Yadegari H, Ivaskevicius V, Oldenburg J, Biswas A. J Thromb Thrombolysis. 2019 Jul;48(1):95-102. doi: 10.1007/s11239-019-01841-w. |
In Silico Analysis of the Subtype Selective Blockage of KCNA Ion Channels through the y-Conotoxins PIIIA, SIIIA, and GIIIA. Kaufmann D, Tietze AA, Tietze D. Mar Drugs. 2019 Mar 19;17(3). pii: E180. doi: 10.3390/md17030180. |
Conjugates of methylene blue with carboline derivatives as new multifunctional agents for the treatment of neurodegenerative diseases. Bachurin SO, Makhaeva GF, Shevtsova EF, Boltneva NP, Kovaleva NV, Lushchekina SV, Rudakova EV, Dubova LG, Vinogradova DV, Sokolov VB, Aksinenko AY, Fisenko VP, Richardson RJ, Aliev G. Sci Rep. 2019 Mar 19;9(1):4873. doi: 10.1038/s41598-019-41272-4. |
Coagulation Factor XIIIa Inhibitor Tridegin: On the Role of Disulfide Bonds for Folding, Stability, and Function. Baeuml CA, Schmitz T, Paul George AA, Sudarsanam M, Hardes K, Steinmetzer T, Holle LA, Wolberg AS, Poetzsch B, Oldenburg J, Biswas A, Imhof D. J Med Chem. 2019 Apr 11;62(7):3513-3523. doi: 10.1021/acs.jmedchem.8b01982. Epub |
A single mutation in cyclodextrin glycosyltransferase from Paenibacillus barengoltzii changes cyclodextrin and maltooligosaccharides production. Castillo J, Caminata Landriel S, Sanchez Costa M, Taboga OA, Berenguer J, Hidalgo A, Ferrarotti SA, Costa H. Protein Eng Des Sel. 2018 Oct 1;31(10):399-407. doi: 10.1093/protein/gzy034. |
Synthesis, In Silico, and In Vitro Evaluation of Long Chain Alkyl Amides from 2-Amino-4-Quinolone Derivatives as Biofilm Inhibitors. Espinosa-Valdes MP, Borbolla-Alvarez S, Delgado-Espinosa AE, Sanchez-Tejeda JF, Ceron-Nava A, Quintana-Romero OJ, Ariza-Castolo A, Garcia-Del Rio DF, Loza-Mejia MA. Molecules. 2019 Jan 17;24(2):327. doi: 10.3390/molecules24020327. |
Ameliorative effects of quercetin against bisphenol A-caused oxidative stress in human erythrocytes: an in vitro and in silico study. Sangai NP, Patel CN, Pandya HA. Toxicol Res (Camb). 2018 Aug 22;7(6):1091-1099. doi: 10.1039/c8tx00105g. |
Primary structures of different isoforms of buffalo pregnancy-associated glycoproteins (BuPAGs) during early pregnancy and elucidation of the 3-dimensional structure of the most abundant isoform BuPAG 7. Lotfan M, Choudhary S, Yadav ML, Kumar S, Singh S, Bathla S, Rawat P, Kaushik JK, Mohanty AK. PLoS One. 2018 Nov 7;13(11):e0206143. doi: 10.1371/journal.pone.0206143. |
In Silico Studies on Compounds Derived from Calceolaria: Phenylethanoid Glycosides as Potential Multitarget Inhibitors for the Development of Pesticides. Loza-Mejia MA, Salazar JR, Sanchez-Tejeda JF. Biomolecules. 2018 Oct 23;8(4):121. doi: 10.3390/biom8040121. |
Arrhythmia mutations in calmodulin cause conformational changes that affect interactions with the cardiac voltage-gated calcium channel. Wang K, Holt C, Lu J, Brohus M, Larsen KT, Overgaard MT, Wimmer R, Van Petegem F. Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):E10556-E10565. doi: |
Mechanistic insights into the host-microbe interaction and pathogen exclusion mediated by the Mucus-binding protein of Lactobacillus plantarum. Singh KS, Kumar S, Mohanty AK, Grover S, Kaushik JK. Sci Rep. 2018 Sep 21;8(1):14198. doi: 10.1038/s41598-018-32417-y. |
Homology models of mouse and rat estrogen receptor-alpha ligand-binding domain created by in silico mutagenesis of a human template: Molecular docking with 17beta-estradiol, diethylstilbestrol, and paraben analogs Gonzaleza TL, Rae JM, Colacino JA, Richardson RJ Computational Toxicology Volume 10, May 2019, Pages 1-16 |
The effect of bisphenol A on testicular steroidogenesis and its amelioration by quercetin: an in vivo and in silico approach. Samova S, Patel CN, Doctor H, Pandya HA, Verma RJ. Toxicol Res (Camb). 2017 Sep 14;7(1):22-31. doi: 10.1039/c7tx00161d. eCollection |
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Metabolites of n-Butylparaben and iso-Butylparaben Exhibit Estrogenic Properties in MCF-7 and T47D Human Breast Cancer Cell Lines. Gonzalez TL, Moos RK, Gersch CL, Johnson MD, Richardson RJ, Koch HM, Rae JM. Toxicol Sci. 2018 Jul 1;164(1):50-59. doi: 10.1093/toxsci/kfy063. |
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VKORC1 and VKORC1L1 have distinctly different oral anticoagulant dose-response characteristics and binding sites. Czogalla KJ, Liphardt K, Hoening K, Hornung V, Biswas A, Watzka M, Oldenburg J. Blood Adv. 2018 Mar 27;2(6):691-702. doi: 10.1182/bloodadvances.2017006775. |
In Vitro and in Vivo Evaluation of 11C-Labeled Azetidinecarboxylates for Imaging Monoacylglycerol Lipase by PET Imaging Studies. Cheng R, Mori W, Ma L, Alhouayek M, Hatori A, Zhang Y, Ogasawara D, Yuan G, Chen Z, Zhang X, Shi H, Yamasaki T, Xie L, Kumata K, Fujinaga M, Nagai Y, Minamimoto T, Svensson M, Wang L, Du Y, Ondrechen MJ, Vasdev N, Cravatt BF, Fowler C, Zhang MR, Liang SH. J Med Chem. 2018 Mar 22;61(6):2278-2291. doi: 10.1021/acs.jmedchem.7b01400 |
Conformational Conotoxin PIIIA Isomers Revisited: Impact of Cysteine Pairing on Disulfide-Bond Assignment and Structure Elucidation. Heimer P, Tietze AA, Baeuml CA, Resemann A, Mayer FJ, Suckau D, Ohlenschlaeger O, Tietze D, Imhof D. Anal Chem. 2018 Mar 6;90(5):3321-3327. doi: 10.1021/acs.analchem.7b04854 |
Prediction of Active Site and Distal Residues in E. coli DNA Polymerase III alpha Polymerase Activity. Parasuram R, Coulther TA, Hollander JM, Keston-Smith E, Ondrechen MJ, Beuning PJ. Biochemistry. 2018 Feb 20;57(7):1063-1072. doi: 10.1021/acs.biochem.7b01004 |
Pharmacophore-based virtual screening of catechol-o-methyltransferase (COMT) inhibitors to combat Alzheimer's disease Patel CN, Georrge JJ, Modi KM, Narechania MB, Patel DP, Gonjalez FJ and Pandya HA J.Biomol.Struct.Dyn.2017 Dec 28. doi: 10.1080/07391102.2017.1404931. |
The structural and functional reliability of Circulins of Chassalia parvifolia for peptide therapeutic scaffolding. Balaraman S, Ramalingam R. J Cell Biochem. 2018 May;119(5):3999-4008. doi: 10.1002/jcb.26557 |
Optimized formulation of NiFe2O4@Ca-alginate composite as a selective and magnetic adsorbent for cationic dyes: Experimental and modeling study Cojocaru C, Humelnicu AC, Samoila P, Pascariu P, Harabagiu V Reactive and Functional Polymers 2018 Apr;125:57-69. doi:10.1016/j.reactfunctpolym.2018.02.008. |
New insights into the mechanism of nickel superoxide degradation from studies of model peptides. Tietze D, Sartorius J, Koley Seth B, Herr K, Heimer P, Imhof D, Mollenhauer D, Buntkowsky G. Sci Rep. 2017 Dec 8;7(1):17194. doi: 10.1038/s41598-017-17446-3. |
Fluorinated Adenosine A2A Receptor Antagonists Inspired by Preladenant as Potential Cancer Immunotherapeutics. Yuan G, Jankins TC, Patrick CG Jr, Philbrook P, Sears O, Hatfield S, Sitkovsky M, Vasdev N, Liang SH, Ondrechen MJ, Pollastri MP, Jones GB. Int J Med Chem. 2017;2017:4852537. doi: 10.1155/2017/4852537 |
Multidrug resistance-associated protein 4 is a bile transporter of Clonorchis sinensis simulated by in silico docking. Dai F, Yoo WG, Lee JY, Lu Y, Pak JH, Sohn WM, Hong SJ. Parasit Vectors. 2017 Nov 21;10(1):578. doi: 10.1186/s13071-017-2523-8. |
Molecular dynamics-assisted pharmacophore modeling of caspase-3-isatin sulfonamide complex: Recognizing essential intermolecular contacts and features of sulfonamide inhibitor class for caspase-3 binding. Kumar SP, Patel CN, Jha PC, Pandya HA. Comput Biol Chem. 2017 Dec;71:117-128. doi: 10.1016/j.compbiolchem.2017.08.006. |
Structure optimization of tetrahydropyridoindole-based aldose reductase inhibitors improved their efficacy and selectivity. Majekova M, Ballekova J, Prnova M, Stefek M. Bioorg Med Chem. 2017 Dec 15;25(24):6353-6360. doi: 10.1016/j.bmc.2017.10.005. |
Structural distortions due to missense mutations in human formylglycine-generating enzyme leading to multiple sulfatase deficiency. Meshach Paul D, Chadah T, Senthilkumar B, Sethumadhavan R, Rajasekaran R. J Biomol Struct Dyn. 2017 Nov 3:1-11. doi: 10.1080/07391102.2017.1394220. |
Identification of novel mutations in congenital afibrinogenemia patients and molecular modeling of missense mutations in Pakistani population. Naz A, Biswas A, Khan TN, Goodeve A, Ahmed N, Saqlain N, Ahmed S, Ujjan ID, Shamsi TS, Oldenburg J. Thromb J. 2017 Sep 12;15:24. doi: 10.1186/s12959-017-0143-3. eCollection 2017. |
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Homology Modeling Inspired Synthesis of 5-HT2A Receptor Inhibitors: A Diazepine Analogue of the Atypical Antipsychotic JL13. Mongeau E, Yuan G, Minden Z, Waldron S, Booth R, Felsing D, Ondrechen MJ, Jones GB. Cent Nerv Syst Agents Med Chem. 2017;17(3):239-244. doi: |
Probing the inhibitory activity of epigallocatechin-gallate on toxic aggregates of mutant (L84F) SOD1 protein through geometry based sampling and steered molecular dynamics. Srinivasan E, Rajasekaran R. J Mol Graph Model. 2017 Jun;74:288-295. doi: 10.1016/j.jmgm.2017.04.019 |
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Theoretical studies on the interaction between the nitrile-based inhibitors and the catalytic triad of Cathepsin K. Pitchumani Violet Mary C, Shankar R, Vijayakumar S. J Biomol Struct Dyn. 2017 Feb 20:1-22. doi: 10.1080/07391102.2017.1289863 |
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Microwave-Assisted ZrSiO2 Catalysed Synthesis, Characterization and Computational Study of Novel Spiro[Indole-Thiazolidines] Derivatives as Anti-tubercular Agents. Borad MA, Bhoi MN, Rathwa SK, Vasava MS, Patel HD, Patel CN, Pandya HA, Pithawala EA, Georrge JJ. Interdiscip Sci. 2018 Jun;10(2):411-418. doi: 10.1007/s12539-016-0195-2. Epub |
Structural, Functional and Phylogenetic Analysis of Sperm Lysozyme-Like Proteins. Kalra S, Pradeep MA, Mohanty AK, Kaushik JK. PLoS One. 2016 Nov 10;11(11):e0166321. doi: 10.1371/journal.pone.0166321. |
Phosphorylation of Cytochrome c Threonine 28 Regulates Electron Transport Chain Activity in Kidney: Implications for AMP Kinase. Mahapatra G, Varughese A, Ji Q, Lee I, Liu J, Vaishnav A, Sinkler C, Kapralov AA, Moraes CT, Sanderson TH, Stemmler TL, Grossman LI, Kagan VE, Brunzelle JS, Salomon AR, Edwards BF, Huettemann M. J Biol Chem. 2016 Oct 7. pii: jbc.M116.744664. |
Computational simulation analysis on human SOD1 mutant (H80R) exposes the structural destabilization and the deviation of Zn binding that directs familial amyotrophic lateral sclerosis. Srinivasan E, Rajasekaran R. J Biomol Struct Dyn. 2017 Sep;35(12):2645-2653. doi: |
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Revisiting the mechanism of coagulation factor XIII activation and regulation from a structure/functional perspective. Gupta S, Biswas A, Akhter MS, Krettler C, Reinhart C, Dodt J, Reuter A, Philippou H, Ivaskevicius V, Oldenburg J. Sci Rep. 2016 Jul 25;6:30105. doi: 10.1038/srep30105. |
In silico approach to explore the disruption in the molecular mechanism of human hyaluronidase 1 by mutant E268K that directs Natowicz syndrome. Meshach Paul D, Rajasekaran R. Eur Biophys J. 2017 Mar;46(2):157-169. doi: 10.1007/s00249-016-1151-0 |
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In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality. Vollan HS, Tannaes T, Vriend G, Bukholm G. Int J Mol Sci. 2016 Apr 21;17(4). pii: E599. doi: 10.3390/ijms17040599. |
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Qualitative and quantitative pharmacophore-similarity assessment of anthranilamide-based factor Xa inhibitors: applications on similar molecules with identical biological endpoints. Kumar SP, Rawal RM, Pandya HA, Jasrai YT. J Recept Signal Transduct Res. 2016;36(2):189-206. doi: |
Homology modeling, functional annotation and comparative genomics of outer membrane protein H of Pasteurella multocida. Ganguly B, Tewari K, Singh R. J Theor Biol. 2015 Dec 7;386:18-24. |
[5-(Benzyloxy)-1H-indol-1-yl]acetic acid, an aldose reductase inhibitor and PPAR ligand. Soltesova Prnova M, Majekova M, Milackova I, Diez-Dacal B, Perez-Sala D, Ceyhan MS, Banerjee S, Stefek M. Acta Biochim Pol. 2015;62(3):523-8. doi: 10.18388/abp.2014_953 |
Receptor-Guided De Novo Design of Dengue Envelope Protein Inhibitors. Desai VH, Kumar SP, Pandya HA, Solanki HA. Appl Biochem Biotechnol. 2015 Oct;177(4):861-78. doi: 10.1007/s12010-015-1784-y. |
Experimental design, modeling and optimization of polyplex formation between DNA oligonucleotides and branched polyethylenimine. Clima L, Ursu EL, Cojocaru C, Rotaru A, Barboiu M, Pinteala M. Org Biomol Chem. 2015 Aug 6. |
Structural and functional influences of coagulation factor XIII subunit B heterozygous missense mutants. Thomas A, Biswas A, Ivaskevicius V, Oldenburg J. Mol Genet Genomic Med. 2015 Jul;3(4):258-71. doi: 10.1002/mgg3.138. Epub 2015 Apr |
200 Structural insights into the theoretical model of Plasmodium falciparum multi drug resistance 1 protein (PfMDR1) and its interaction with phytochemicals as efficacious antimalarial drugs: an in silico and in vitro approach. Patel SK, Jha PC, Jasrai Y, Pandya HA, George L. J Biomol Struct Dyn. 2015;33 Suppl 1:132-4. doi: 10.1080/07391102.2015.1032837. |
Prediction of protein targets of kinetin using in silico and in vitro methods: a case study on spinach seed germination mechanism. Kumar SP, Parmar VR, Jasrai YT, Pandya HA. J Chem Biol. 2015 May 12;8(3):95-105. doi: 10.1007/s12154-015-0135-3. eCollection |
The effect of various atomic partial charge schemes to elucidate consensus activity-correlating molecular regions: a test case of diverse QSAR models. Kumar SP, Jha PC, Jasrai YT, Pandya HA. J Biomol Struct Dyn. 2016;34(3):540-59. doi: 10.1080/07391102.2015.1044474 |
Computational docking simulations of a DNA-aptamer for argininamide and related ligands. Albada HB, Golub E, Willner I. J Comput Aided Mol Des. 2015 Jul;29(7):643-54. doi: 10.1007/s10822-015-9844-5. |
Taming molecular flexibility to tackle rare diseases. Cubellis MV, Baaden M, Andreotti G. Biochimie. 2015 Jun;113:54-8. doi: 10.1016/j.biochi.2015.03.018 |
![]() Krieger E, Vriend G. J Comput Chem. 2015 May 15;36(13):996-1007 The open access article is available here, more details about the cover can be found here. |
Inter-locus as well as intra-locus heterogeneity in LINE-1 promoter methylation in common human cancers suggests selective demethylation pressure at specific CpGs. Nuesgen N, Goering W, Dauksa A, Biswas A, Jamil MA, Dimitriou I, Sharma A, Singer H, Fimmers R, Froehlich H, Oldenburg J, Gulbinas A, Schulz WA, El-Maarri O. Clin Epigenetics. 2015 Mar 1;7(1):17. doi: 10.1186/s13148-015-0051-y. eCollection |
Molecular interaction of selected phytochemicals under the charged environment of Plasmodium falciparum chloroquine resistance transporter (PfCRT) model. Patel SK, Khedkar VM, Jha PC, Jasrai YT, Pandya HA, George LB, Highland HN, Skelton AA. J Biomol Struct Dyn. 2016;34(2):290-303. doi: 10.1080/07391102.2015.1028449 |
Synthesis and evaluation of 2-halogenated-1,1-bis(4-hydroxyphenyl)-2-(3-hydroxyphenyl)-ethylenes as potential estrogen receptor-targeted radiodiagnostic and radiotherapeutic agents. Hanson RN, Tongcharoensirikul P, Barnsley K, Ondrechen MJ, Hughes A, DeSombre ER. Steroids. 2015 Apr;96:50-62. |
A comprehensive molecular dynamics approach to protein retention modeling in ion exchange chromatography. Lang KM, Kittelmann J, Durr C, Osberghaus A, Hubbuch J. J Chromatogr A. 2015 Feb 13;1381:184-93. doi: 10.1016/j.chroma.2015.01.018 |
Pocketome of human kinases: prioritizing the ATP binding sites of (yet) untapped protein kinases for drug discovery. Volkamer A, Eid S, Turk S, Jaeger S, Rippmann F, Fulle S. J Chem Inf Model. 2015 Mar 23;55(3):538-49. doi: 10.1021/ci500624s |
Rutin stimulates sarcoplasmic reticulum Ca(2+)-ATPase activity (SERCA1) and protects SERCA1 from peroxynitrite mediated injury. Viskupicova J, Strosova MK, Zizkova P, Majekova M, Horakova L. Mol Cell Biochem. 2015 Apr;402(1-2):51-62. doi: 10.1007/s11010-014-2313-y |
Rational Design of Alpha-Helical Antimicrobial Peptides: Do's and Don'ts. Uggerhoj LE, Poulsen TJ, Munk JK, Fredborg M, Sondergaard TE, Frimodt-Moller N, Hansen PR, Wimmer R. Chembiochem. 2015 Jan 19;16(2):242-53. doi: 10.1002/cbic.201402581 |
Positioning of cysteine residues within the N-terminal portion of the BST-2/tetherin ectodomain is important for functional dimerization of BST-2. Welbourn S, Kao S, Du Pont KE, Andrew AJ, Berndsen CE, Strebel K. J Biol Chem. 2015 Feb 6;290(6):3740-51. doi: 10.1074/jbc.M114.617639 |
Inhibition of the sarco/endoplasmic reticulum Ca2+-ATPase (SERCA1) by rutin derivatives. Viskupicova J, Majekova M, Horakova L. J Muscle Res Cell Motil. 2015 Apr;36(2):183-94. doi: 10.1007/s10974-014-9402-0. |
Novel insights into structure and function of factor XIIIa-inhibitor tridegin. Boehm M, Baeuml CA, Hardes K, Steinmetzer T, Roeser D, Schaub Y, Than ME, Biswas A, Imhof D. J Med Chem. 2014 Dec 26;57(24):10355-65. doi: 10.1021/jm501058g |
Molecular simulation studies of human coagulation factor VIII C domain-mediated membrane binding. Du J, Wichapong K, Hackeng TM, Nicolaes GA. Thromb Haemost. 2014 Oct 30;113(2). |
A series of PDB-related databanks for everyday needs. Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G. Nucleic Acids Res. 2015 Jan;43(Database issue):D364-8. doi: 10.1093/nar/gku1028. |
Understanding the functional difference between growth arrest-specific protein 6 and protein S: an evolutionary approach. Studer RA, Opperdoes FR, Nicolaes GA, Mulder AB, Mulder R. Open Biol. 2014 Oct;4(10). pii: 140121. doi: 10.1098/rsob.140121. |
Structural and functional characterization of the R-modules in alginate C-5 epimerases AlgE4 and AlgE6 from Azotobacter vinelandii. Buchinger E, Knudsen DH, Behrens MA, Pedersen JS, Aarstad OA, Tondervik A, Valla S, Skjak-Braek G, Wimmer R, Aachmann FL. J Biol Chem. 2014 Nov 7;289(45):31382-96. doi: 10.1074/jbc.M114.567008 |
Crystal structure of patatin-17 in complex with aged and non-aged organophosphorus compounds. Wijeyesakere SJ, Richardson RJ, Stuckey JA. PLoS One. 2014 Sep 23;9(9):e108245. doi: 10.1371/journal.pone.0108245. |
With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase. Silva PJ. PeerJ. 2014 Sep 2;2:e551. doi: 10.7717/peerj.551. eCollection 2014. |
NLRP7 inter-domain interactions: the NACHT-associated domain is the physical mediator for oligomeric assembly. Singer H, Biswas A, Zimmer N, Messaed C, Oldenburg J, Slim R, El-Maarri O. Mol Hum Reprod. 2014 Oct;20(10):990-1001. doi: 10.1093/molehr/gau060 |
Structural features of peptoid-peptide hybrids in lipid-water interfaces. Uggerhoj LE, Munk JK, Hansen PR, Guentert P, Wimmer R. FEBS Lett. 2014 Aug 25;588(17):3291-7. doi: 10.1016/j.febslet.2014.07.016 |
A cell-permeable inhibitor to trap g-alpha-q proteins in the empty pocket conformation. Schmitz AL, Schrage R, Gaffal E, Charpentier TH, Wiest J, Hiltensperger G, Morschel J, Hennen S, Haeussler D, Horn V, Wenzel D, Grundmann M, Buellesbach KM, Schroeder R, Brewitz HH, Schmidt J, Gomeza J, Gales C, Fleischmann BK, Tueting T, Imhof D, Tietze D, Guetschow M, Holzgrabe U, Sondek J, Harden TK, Mohr K, Kostenis E. Chem Biol. 2014 Jul 17;21(7):890-902. doi: 10.1016/j.chembiol.2014.06.003. |
Refined Mapping of a Hypertension Susceptibility Locus on Rat Chromosome 12. Prisco SZ, Prokop JW, Sarkis AB, Yeo NC, Hoffman MJ, Hansen CC, Jacob HJ, Flister MJ, Lazar J. Hypertension. 2014 Jul 7. pii: HYPERTENSIONAHA.114.03550. |
Computational development of rubromycin-based lead compounds for HIV-1 reverse transcriptase inhibition Bernardo CEP, Silva PJ PeerJ 2014 2:e470 |
YASARA View - molecular graphics for all devices - from smartphones to workstations. Krieger E, Vriend G. Bioinformatics. 2014 Oct 15;30(20):2981-2. doi: 10.1093/bioinformatics/btu426. |
Computational library design for increasing haloalkane dehalogenase stability. Floor RJ, Wijma HJ, Colpa DI, Ramos-Silva A, Jekel PA, Szymaski W, Feringa BL, Marrink SJ, Janssen DB. Chembiochem. 2014 Jul 21;15(11):1660-72. doi: 10.1002/cbic.201402128 |
The Arg98Trp mutation in human VKORC1 causing VKCFD2 disrupts a di-arginine-based ER retention motif. Czogalla KJ, Biswas A, Rost S, Watzka M, Oldenburg J. Blood. 2014 Aug 21;124(8):1354-62. doi: 10.1182/blood-2013-12-545988 |
Novel kv7.1-phosphatidylinositol 4,5-bisphosphate interaction sites uncovered by charge neutralization scanning. Eckey K, Wrobel E, Strutz-Seebohm N, Pott L, Schmitt N, Seebohm G. J Biol Chem. 2014 Aug 15;289(33):22749-58. doi: 10.1074/jbc.M114.589796. |
Computationally efficient and accurate enantioselectivity modeling by clusters of molecular dynamics simulations. Wijma HJ, Marrink SJ, Janssen DB. J Chem Inf Model. 2014 Jul 28;54(7):2079-92. doi: 10.1021/ci500126x |
Eight novel F13A1 gene missense mutations in patients with mild FXIII deficiency: in silico analysis suggests changes in FXIII-A subunit structure/function. Biswas A, Ivaskevicius V, Thomas A, Varvenne M, Brand B, Rott H, Haussels I, Ruehl H, Scholz U, Klamroth R, Oldenburg J. Ann Hematol. 2014 Oct;93(10):1665-76. doi: 10.1007/s00277-014-2102-4 |
Molecular evolution of GPCRs: Melanocortin/melanocortin receptors. Dores RM, Londraville RL, Prokop J, Davis P, Dewey N, Lesinski N. J Mol Endocrinol. 2014 Jun;52(3):T29-42. doi: 10.1530/JME-14-0050. |
Implementation of pseudoreceptor-based pharmacophore queries in the prediction of probable protein targets: explorations in the protein structural profile of Zea mays. Kumar SP, Jha PC, Pandya HA, Jasrai YT. Mol Biosyst. 2014 Jul;10(7):1833-44. doi: 10.1039/c4mb00058g |
Development of pharmacophore similarity-based quantitative activity hypothesis and its applicability domain: applied on a diverse data-set of HIV-1 integrase inhibitors. Kumar SP, Jasrai YT, Mehta VP, Pandya HA. J Biomol Struct Dyn. 2015;33(4):706-22. doi: 10.1080/07391102.2014.908142 |
2-Chloro-1,4-naphthoquinone derivative of quercetin as an inhibitor of aldose reductase and anti-inflammatory agent. Milackova I, Prnova MS, Majekova M, Sotnikova R, Stasko M, Kovacikova L, Banerjee S, Veverka M, Stefek M. J Enzyme Inhib Med Chem. 2015 Feb;30(1):107-13. doi: |
Discovery of the elusive leptin in birds: identification of several 'missing links' in the evolution of leptin and its receptor. Prokop JW, Schmidt C, Gasper D, Duff RJ, Milsted A, Ohkubo T, Ball HC, Shawkey MD, Mays HL Jr, Cogburn LA, Londraville RL. PLoS One. 2014 Mar 24;9(3):e92751. doi: 10.1371/journal.pone.0092751. eCollection |
Stabilization of cyclohexanone monooxygenase by a computationally designed disulfide bond spanning only one residue. van Beek HL, Wijma HJ, Fromont L, Janssen DB, Fraaije MW. FEBS Open Bio. 2014 Feb 3;4:168-74. doi: 10.1016/j.fob.2014.01.009. eCollection |
The lantibiotic NAI-107 binds to bactoprenol-bound cell wall precursors and impairs membrane functions. Muench D, Mueller A, Schneider T, Kohl B, Wenzel M, Bandow JE, Maffioli S, Sosio M, Donadio S, Wimmer R, Sahl HG. J Biol Chem. 2014 Apr 25;289(17):12063-76. doi: 10.1074/jbc.M113.537449 |
A computational model for non-conserved mature miRNAs from the rice genome. Kumar SP, Pandya HA, Jasrai YT. SAR QSAR Environ Res. 2014;25(3):205-20. doi: 10.1080/1062936X.2013.875941 |
Compound prioritization from inverse docking experiment using receptor-centric and ligand-centric methods: a case study on Plasmodium falciparum Fab enzymes. Kumar SP, Pandya HA, Desai VH, Jasrai YT. J Mol Recognit. 2014 Apr;27(4):215-29. doi: 10.1002/jmr.2353. |
LIMD2 is a small LIM-only protein overexpressed in metastatic lesions that regulates cell motility and tumor progression by directly binding to and activating the integrin-linked kinase. Peng H, Talebzadeh-Farrooji M, Osborne MJ, Prokop JW, McDonald PC, Karar J, Hou Z, He M, Kebebew E, Orntoft T, Herlyn M, Caton AJ, Fredericks W, Malkowicz B, Paterno CS, Carolin AS, Speicher DW, Skordalakes E, Huang Q, Dedhar S, Borden KL, Rauscher FJ 3rd. Cancer Res. 2014 Mar 1;74(5):1390-403. doi: 10.1158/0008-5472.CAN-13-1275. |
Structural and functional insights into the catalytic inactivity of the major fraction of buffalo milk xanthine oxidoreductase. Gadave KS, Panda S, Singh S, Kalra S, Malakar D, Mohanty AK, Kaushik JK. PLoS One. 2014 Jan 31;9(1):e87618 |
Blocking CD40-TRAF6 signaling is a therapeutic target in obesity-associated insulin resistance. Chatzigeorgiou A, Seijkens T, Zarzycka B, Engel D, Poggi M, van den Berg S, van den Berg S, Soehnlein O, Winkels H, Beckers L, Lievens D, Driessen A, Kusters P, Biessen E, Garcia-Martin R, Klotzsche-von Ameln A, Gijbels M, Noelle R, Boon L, Hackeng T, Schulte KM, Xu A, Vriend G, Nabuurs S, Chung KJ, Willems van Dijk K, Rensen PC, Gerdes N, de Winther M, Block NL, Schally AV, Weber C, Bornstein SR, Nicolaes G, Chavakis T, Lutgens E. Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2686-91. doi: |
Parallel pathways for nitrite reduction during anaerobic growth in Thermus thermophilus. Alvarez L, Bricio C, Hidalgo A, Berenguer J. J Bacteriol. 2014 Apr;196(7):1350-8. doi: 10.1128/JB.01042-13. Epub 2014 Jan 17. |
Computationally designed libraries for rapid enzyme stabilization. Wijma HJ, Floor RJ, Jekel PA, Baker D, Marrink SJ, Janssen DB. Protein Eng Des Sel. 2014 Feb;27(2):49-58. doi: 10.1093/protein/gzt061 |
Structural basis of PI(4,5)P2-dependent regulation of GluA1 by phosphatidylinositol-5-phosphate 4-kinase, type II, alpha (PIP5K2A). Seebohm G, Wrobel E, Pusch M, Dicks M, Terhag J, Matschke V, Rothenberg I, Ursu ON, Hertel F, Pott L, Lang F, Schulze-Bahr E, Hollmann M, Stoll R, Strutz-Seebohm N. Pflugers Arch. 2014 Jan 5. |
Genetic variation in the two-pore domain potassium channel, TASK-1, may contribute to an atrial substrate for arrhythmogenesis. Liang B, Soka M, Christensen AH, Olesen MS, Larsen AP, Knop FK, Wang F, Nielsen JB, Andersen MN, Humphreys D, Mann SA, Huttner IG, Vandenberg JI, Svendsen JH, Haunso S, Preiss T, Seebohm G, Olesen SP, Schmitt N, Fatkin D. J Mol Cell Cardiol. 2014 Feb;67:69-76 |
The drug diazaborine blocks ribosome biogenesis by inhibiting the AAA-ATPase Drg1. Loibl M, Klein I, Prattes M, Schmidt C, Kappel L, Zisser G, Gungl A, Krieger E, Pertschy B, Bergler H. J Biol Chem. 2014 Feb 14;289(7):3913-22. doi: 10.1074/jbc.M113.536110 |
A complex partnership: KCNQ1 and KCNE1. Seebohm G. Biophys J. 2013 Dec 3;105(11):2437-8. |
Severe congenital factor XIII deficiency caused by novel W187X and G273V mutations in the F13A gene; diagnosis and classification according to the ISTH/SSC guidelines. Souri M, Biswas A, Misawa M, Omura H, Ichinose A. Haemophilia. 2014 Mar;20(2):255-62 |
Pharmacophore-similarity-based QSAR (PS-QSAR) for group-specific biological activity predictions. Prasanth Kumar S, Jasrai YT, Pandya HA, Rawal RM. J Biomol Struct Dyn. 2015;33(1):56-69. doi: 10.1080/07391102.2013.849618 |
Analysis of Sry duplications on the Rattus norvegicus Y-chromosome. Prokop JW, Underwood AC, Turner ME, Miller N, Pietrzak D, Scott S, Smith C, Milsted A. BMC Genomics. 2013 Nov 14;14:792. doi: 10.1186/1471-2164-14-792. |
Favorable adsorption of capped amino acids on graphene substrate driven by desolvation effect. Dragneva N, Floriano WB, Stauffer D, Mawhinney RC, Fanchini G, Rubel O. J Chem Phys. 2013 Nov 7;139(17):174711 |
Inhibition of CIN85-mediated invasion by a novel SH3 domain binding motif in the lysyl oxidase propeptide. Sato S, Zhao Y, Imai M, Simister PC, Feller SM, Trackman PC, Kirsch KH, Sonenshein GE. PLoS One. 2013 Oct 22;8(10):e77288. doi: 10.1371/journal.pone.0077288. |
CSF1R mutations in hereditary diffuse leukoencephalopathy with spheroids are loss of function. Pridans C, Sauter KA, Baer K, Kissel H, Hume DA. Sci Rep. 2013 Oct 22;3:3013. doi: 10.1038/srep03013. |
MAS promoter regulation: a role for Sry and tyrosine nitration of the KRAB domain of ZNF274 as a feedback mechanism. Prokop JW, Rauscher FJ 3rd, Peng H, Liu Y, Araujo FC, Watanabe I, Reis FM, Milsted A. Clin Sci (Lond). 2014 May;126(10):727-38. doi: 10.1042/CS20130385. |
Design and evaluation of xanthine based adenosine receptor antagonists: potential hypoxia targeted immunotherapies. Thomas R, Lee J, Chevalier V, Sadler S, Selesniemi K, Hatfield S, Sitkovsky M, Ondrechen MJ, Jones GB. Bioorg Med Chem. 2013 Dec 1;21(23):7453-64. |
Engineering and kinetic stabilization of the therapeutic enzyme Anabeana variabilis phenylalanine ammonia lyase. Jaliani HZ, Farajnia S, Mohammadi SA, Barzegar A, Talebi S. Appl Biochem Biotechnol. 2013 Dec;171(7):1805-18 |
Human VKORC1 mutations cause variable degrees of 4-hydroxycoumarin resistance and affect putative warfarin binding interfaces. Czogalla KJ, Biswas A, Wendeln AC, Westhofen P, Mueller CR, Watzka M, Oldenburg J. Blood. 2013 Oct 10;122(15):2743-50 |
The preferred conformation of dipeptides in the context of biosynthesis. Bywater RP, Veryazov V. Naturwissenschaften. 2013 Sep;100(9):853-9 |
The linker pivot in Ci-VSP: the key to unlock catalysis. Hobiger K, Utesch T, Mroginski MA, Seebohm G, Friedrich T. PLoS One. 2013 Jul 29;8(7):e70272 |
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. Cereto-Massague A, Ojeda MJ, Joosten RP, Valls C, Mulero M, Salvado MJ, Arola-Arnal A, Arola L, Garcia-Vallve S, Pujadas G. J Cheminform. 2013 Jul 29;5(1):36 |
Unraveling the photoluminescence response of light-switching ruthenium(II) complexes bound to amyloid-beta. Cook NP, Ozbil M, Katsampes C, Prabhakar R, Marti AA. J Am Chem Soc. 2013 Jul 24;135(29):10810-6 |
A common structural component for beta-subunit mediated modulation of slow inactivation in different KV channels. Strutz-Seebohm N, Henrion U, Schmitt N, Schulze-Bahr E, Seebohm G. Cell Physiol Biochem. 2013;31(6):968-80 |
Redesign of a Phenylalanine Aminomutase into a Phenylalanine Ammonia Lyase Bartsch S, Wybenga GG, Jansen M, Heberling MM, Wu B, Dijkstra BW, Janssen DB ChemCatChem 5,1797-1802 |
A plant homolog of animal glutamate receptors is an ion channel gated by multiple hydrophobic amino acids. Tapken D, Anschuetz U, Liu LH, Huelsken T, Seebohm G, Becker D, Hollmann M. Sci Signal. 2013 Jun 11;6(279):ra47 |
Differential mechanisms of activation of the Ang peptide receptors AT1, AT2, and MAS: using in silico techniques to differentiate the three receptors. Prokop JW, Santos RA, Milsted A. PLoS One. 2013 Jun 3;8(6):e65307. doi: 10.1371/journal.pone.0065307. Print 2013. |
A method for in silico identification of SNAIL/SLUG DNA binding potentials to the E-box sequence using molecular dynamics and evolutionary conserved amino acids. Prokop JW, Liu Y, Milsted A, Peng H, Rauscher FJ 3rd. J Mol Model. 2013 Sep;19(9):3463-9. doi: 10.1007/s00894-013-1876-y |
Structural insights into the theoretical model of Plasmodium falciparum NADH dehydrogenase and its interaction with artemisinin and derivatives: towards global health therapeutics. Kumar SP, Jasrai YT, Pandya HA, George LB, Patel SK. OMICS. 2013 May;17(5):231-41. doi: 10.1089/omi.2012.0129. |
Soluble polysialylated NCAM: a novel player of the innate immune system in the lung. Ulm C, Saffarzadeh M, Mahavadi P, Mueller S, Prem G, Saboor F, Simon P, Middendorff R, Geyer H, Henneke I, Bayer N, Rinne S, Luetteke T, Boettcher-Friebertshaeuser E, Gerardy-Schahn R, Schwarzer D, Muehlenhoff M, Preissner KT, Guenther A, Geyer R, Galuska SP. Cell Mol Life Sci. 2013 Oct;70(19):3695-708. doi: 10.1007/s00018-013-1342-0 |
Insights into pathological mechanisms of missense mutations in C-Terminal domains of von Willebrand factor causing qualitative or quantitative von Willebrand disease Yadegari H, Driesen J, Pavlova A, Biswas A, Ivaskevicius V, Klamroth R, Oldenburg J Haematologica. 2013 Mar 28 |
A conserved threonine in the S1-S2 loop of K(V)7.2 and K (V)7.3 channels regulates voltage-dependent activation. Fuell Y, Seebohm G, Lerche H, Maljevic S. Pflugers Arch. 2012 Dec 28. |
The size and conservation of a coiled-coil structure in the ectodomain of human BST-2/tetherin is dispensable for inhibition of HIV-1 virion release. Andrew AJ, Berndsen CE, Kao S, Strebel K. J Biol Chem. 2012 Dec 28;287(53):44278-88. doi: 10.1074/jbc.M112.418822 |
NMR structure of a lytic polysaccharide monooxygenase provides insight into copper binding, protein dynamics, and substrate interactions Aachmann FL, Sorlie M, Skjak-Braek G, Eijsink VG, Vaaje-Kolstad G Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18779-84 An NMR structure determined with the help of YASARA, PDB ID 2LHS |
Eurocin, a new fungal defensin: structure, lipid binding, and its mode of action Oeemig JS, Lynggaard C, Knudsen DH, Hansen FT, Norgaard KD, Schneider T, Vad BS, Sandvang DH, Nielsen LA, Neve S, Kristensen HH, Sahl HG, Otzen DE, Wimmer R J Biol Chem. 2012 Dec 7;287(50):42361-72 An NMR structure determined with the help of YASARA, PDB ID 2LT8 |
Leptin and leptin receptor: analysis of a structure to function relationship in interaction and evolution from humans to fish. Prokop JW, Duff RJ, Ball HC, Copeland DL, Londraville RL. Peptides. 2012 Dec;38(2):326-36. doi: 10.1016/j.peptides.2012.10.002 |
Effects of non-catalytic, distal amino acid residues on activity of E. coli DinB (DNA polymerase IV). Walsh JM, Parasuram R, Rajput PR, Rozners E, Ondrechen MJ, Beuning PJ. Environ Mol Mutagen. 2012 Dec;53(9):766-76. |
Post-translational S-nitrosylation is an endogenous factor fine tuning the properties of human S100A1 protein Lenarcic A, Zivkovi M, Zareba-Koziol M, Zhukova L, Poznanski J, Zhukov I, Wyslouch-Cieszynska A J Biol Chem. 2012 Nov 23;287(48):40457-70 An NMR structure determined with the help of YASARA, PDB ID 2LLU |
CING: an integrated residue-based structure validation program suite. Doreleijers JF, Sousa da Silva AW, Krieger E, Nabuurs SB, Spronk CA, Stevens TJ, Vranken WF, Vriend G, Vuister GW. J Biomol NMR. 2012 Nov;54(3):267-83. doi: 10.1007/s10858-012-9669-7 |
Structural rearrangements at physiological pH: nuclear magnetic resonance insights from the V210I human prion protein mutant Biljan I, Ilc G, Giachin G, Plavec J, Legname G Biochemistry. 2012 Sep 25;51(38):7465-74 An NMR structure determined with the help of YASARA, PDB ID 2LV1 |
The human Aurora kinase inhibitor danusertib is a lead compound for anti-trypanosomal drug discovery via target repurposing. Ochiana SO, Pandarinath V, Wang Z, Kapoor R, Ondrechen MJ, Ruben L, Pollastri MP. Eur J Med Chem. 2013 Apr;62:777-84. |
The KCNE Tango - How KCNE1 Interacts with Kv7.1. Wrobel E, Tapken D, Seebohm G. Front Pharmacol. 2012;3:142 |
Protein folding: a problem with multiple solutions. Bywater RP. J Biomol Struct Dyn. 2013 Apr;31(4):351-62 |
Accelerated simulation of unfolding and refolding of a large single chain globular protein. Seddon GM, Bywater RP. Open Biol. 2012 Jul;2(7):120087 |
Inactivation and reactivation of ribonuclease A studied by computer simulation. Seddon GM, Bywater RP. Open Biol. 2012 Jul;2(7):120088 |
NMR structure note: solution structure of Ca2+ binding domain 2B of the third isoform of the Na+/Ca2+ exchanger Breukels V, Touw WG, Vuister GW J Biomol NMR. 2012 Sep;54(1):115-21 An NMR structure determined with the help of YASARA, PDB ID 2LT9 |
Motion of transfer RNA from the A/T state into the A-site using docking and simulations Caulfield T, Devkota B Proteins. 2012 Nov;80(11):2489-500 |
Structural basis for the protective effect of the human prion protein carrying the dominant-negative E219K polymorphism Biljan I, Giachin G, Ilc G, Zhukov I, Plavec J, Legname G Biochem J. 2012 Sep 1;446(2):243-51 An NMR structure determined with the help of YASARA, PDB IDs 2LFT and 2LSB |
POOL server: machine learning application for functional site prediction in proteins. Somarowthu S, Ondrechen MJ. Bioinformatics. 2012 Aug 1;28(15):2078-9. |
The Catalytic Machinery of Rhomboid Proteases: Combined MD and QM Simulation Uritsky N, Shokhen M, Albeck A J Chem Theory Comput |
Overlapping cardiac phenotype associated with a familial mutation in the voltagesensor of the KCNQ1 channel. Henrion U, Zumhagen S, Steinke K, Strutz-Seebohm N, Stallmeyer B, Lang F, Schulze-Bahr E, Seebohm G. Cell Physiol Biochem. 2012;29(5-6):809-18 |
Amino acid function and docking site prediction through combining disease variants, structure alignments, sequence alignments, and molecular dynamics: a study of the HMG domain. Prokop JW, Leeper TC, Duan ZH, Milsted A. BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S3. doi: 10.1186/1471-2105-13-S2-S3. |
X-ray structures of the progesterone receptor ligand-binding domain in its agonist state reveal differing mechanisms for the mixed profiles of 11b-substituted steroids Lusher SJ, Raaijmakers HC, Vu Pham D, Kazemier B, Bosch R, McGuire R, Azevedo R, Dechering K, Oubrie A, van Duin M, de Vlieg J J Biol Chem. 2012 Apr 25 |
PDB_REDO: constructive validation, more than just looking for errors Joosten RP, Joosten K, Murshudov GN, Perrakis A Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):484-96 |
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Identification of a novel signaling pathway and its relevance for GluA1 recycling. Seebohm G, Neumann S, Theiss C, Novkovic T, Hill EV, Tavare JM, Lang F, Hollmann M, Manahan-Vaughan D, Strutz-Seebohm N. PLoS One. 2012;7(3):e33889 |
Novel Mutation in Spectrin-like Repeat 1 of Dystrophin Central Domain Causes Protein Misfolding and Mild Becker Muscular Dystrophy Acsadi G, Moore SA, Cheron A, Delalande O, Bennett L, Kupsky W, El-Baba M, Le Rumeur E, Hubert JF J Biol Chem. 2012 May 25;287(22):18153-62 |
Structurally diverse y-conotoxin PIIIA isomers block sodium channel NaV 1.4 Tietze AA, Tietze D, Ohlenschlaeger O, Leipold E, Ullrich F, Kuehl T, Mischo A, Buntkowsky G, Goerlach M, Heinemann SH, Imhof D Angew Chem Int Ed Engl. 2012 Apr 23;51(17):4058-61 |
Goodpasture antigen-binding protein/ceramide transporter binds to human serum amyloid P-component and is present in brain amyloid plaques. Mencarelli C, Bode GH, Losen M, Kulharia M, Molenaar PC, Veerhuis R, Steinbusch HW, De Baets MH, Nicolaes GA, Martinez-Martinez P. J Biol Chem. 2012 Apr 27;287(18):14897-911. doi: 10.1074/jbc.M111.299545 |
Evolution of the voltage sensor domain of the voltage-sensitive phosphoinositide phosphatase, VSP/TPTE, suggests a role as a proton channel in eutherian mammals Sutton KA, Jungnickel MK, Jovine L, Florman HM. Mol Biol Evol. 2012 Mar 6 |
On dating stages in prebiotic chemical evolution. Bywater RP. Naturwissenschaften. 2012 Mar;99(3):167-76 |
The insect defensin lucifensin from Lucilia sericata Nygaard MK, Andersen AS, Kristensen HH, Krogfelt KA, Fojan P, Wimmer R J Biomol NMR. 2012 Mar;52(3):277-82 An NMR structure determined with the help of YASARA, PDB ID 2LLD |
From rat to human: regulation of Renin-Angiotensin system genes by sry. Prokop JW, Watanabe IK, Turner ME, Underwood AC, Martins AS, Milsted A. Int J Hypertens. 2012;2012:724240. doi: 10.1155/2012/724240 |
Directed evolution strategies for enantiocomplementary haloalkane dehalogenases: from chemical waste to enantiopure building blocks van Leeuwen JG, Wijma HJ, Floor RJ, van der Laan JM, Janssen DB Chembiochem. 2012 Jan 2;13(1):137-48 |
Mixed inhibition of adenosine deaminase activity by 1,3-dinitrobenzene: a model for understanding cell-selective neurotoxicity in chemically-induced energy deprivation syndromes in brain Wang Y, Liu X, Schneider B, Zverina EA, Russ K, Wijeyesakere SJ, Fierke CA, Richardson RJ, Philbert MA Toxicol Sci. 2012 Feb;125(2):509-21 |
Pharmacological validation of Trypanosoma brucei phosphodiesterases B1 and B2 as druggable targets for African sleeping sickness. Bland ND, Wang C, Tallman C, Gustafson AE, Wang Z, Ashton TD, Ochiana SO, McAllister G, Cotter K, Fang AP, Gechijian L, Garceau N, Gangurde R, Ortenberg R, Ondrechen MJ, Campbell RK, Pollastri MP. J Med Chem. 2011 Dec 8;54(23):8188-94.. |
Altered stress stimulation of inward rectifier potassium channels in Andersen-Tawil syndrome. Seebohm G, Strutz-Seebohm N, Ursu ON, Preisig-Mueller R, Zuzarte M, Hill EV,Kienitz MC, Bendahhou S, Fauler M, Tapken D, Decher N, Collins A, Jurkat-Rott K,Steinmeyer K, Lehmann-Horn F, Daut J, Tavare JM, Pott L, Bloch W, Lang F. FASEB J. 2012 Feb;26(2):513-22 |
Homology modeling and functional annotation of bubaline pregnancy associated glycoprotein 2 Ganguly B and Prasad S Journal of Animal Science and Biotechnology 2012, 3:13 |
Molecular Docking of Aromatase Inhibitors Suvannang N, Nantasenamat C, Isarankura-Na-Ayudhya C, Prachayasittikul V Molecules 2011, 16(5):3597-3617 |
A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase. Somarowthu S, Brodkin HR, D'Aquino JA, Ringe D, Ondrechen MJ, Beuning PJ. Biochemistry. 2011 Nov 1;50(43):9283-95. |
Enzyme closure and nucleotide binding structurally lock guanylate kinase Delalande O, Sacquin-Mora S, Baaden M Biophys J. 2011 Sep 21;101(6):1440-9 |
Plasmin substrate binding site cooperativity guides the design of potent peptide aldehyde inhibitors Swedberg JE, Harris JM Biochemistry. 2011 Oct 4;50(39):8454-62 |
Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators Lusher SJ, Raaijmakers HC, Vu-Pham D, Dechering K, Lam TW, Brown AR, Hamilton NM, Nimz O, Bosch R, McGuire R, Oubrie A, de Vlieg J J Biol Chem. 2011 Oct 7;286(40):35079-86 |
Toward the molecular basis of inherited prion diseases: NMR structure of the human prion protein with V210I mutation Biljan I, Ilc G, Giachin G, Raspadori A, Zhukov I, Plavec J, Legname G J Mol Biol. 2011 Sep 30;412(4):660-73 An NMR structure determined with the help of YASARA, PDB ID 2LEJ |
Structural basis of slow activation gating in the cardiac I Ks channel complex. Strutz-Seebohm N, Pusch M, Wolf S, Stoll R, Tapken D, Gerwert K, Attali B,Seebohm G. Cell Physiol Biochem. 2011;27(5):443-52 |
Molecular Docking of Aromatase Inhibitors Suvannang N, Nantasenamat C, Isarankura-Na-Ayudhya C, Prachayasittikul V Molecules 2011, 16(5), 3597-3617 |
Mastering the canonical loop of serine protease inhibitors: enhancing potency by optimising the internal hydrogen bond network Swedberg JE, de Veer SJ, Sit KC, Reboul CF, Buckle AM, Harris JM PLoS One. 2011 Apr 27;6(4):e19302 |
How to remain nonfolded and pliable: the linkers in modular alpha-amylases as a case study. Feller G, Dehareng D, Lage JL FEBS J. 2011 Jul;278(13):2333-40 |
Inhibition of Kir2.1 (KCNJ2) by the AMP-activated protein kinase. Alesutan I, Munoz C, Sopjani M, Dermaku-Sopjani M, Michael D, Fraser S, Kemp BE, Seebohm G, Foeller M, Lang F. Biochem Biophys Res Commun. 2011 May 20;408(4):505-10 |
Aminoacyl-coenzyme A synthesis catalyzed by a CoA ligase from Penicillium chrysogenum Koetsier MJ, Jekel PA, Wijma HJ, Bovenberg RA, Janssen DB FEBS Lett. 2011 Mar 23;585(6):893-8 |
Computational characterization of the substrate-binding mode in coproporphyrinogen III oxidase Silva PJ, Ramos MJ J Phys Chem B. 2011 Mar 3;115(8):1903-10 |
Enantioselective CuII-Catalyzed Diels-Alder and Michael Addition Reactions in Water Using Bio-Inspired Triazacyclophane-Based Ligands Bauke Albada H, Rosati F, Coquiere D, Roelfes G, Liskamp RM Eur J Org Chem 2011:1714-1720 |
The Molecular Basis of Sex: Linking Yeast to Human Swanson WJ, Aagaard JE, Vacquier VD, Monne M, Al Hosseini HS, Jovine L Mol Biol Evol. 2011 Jan 31 |
Kinetic Resolution of alpha-Bromoamides: Experimental and Theoretical Investigation of Highly Enantioselective Reactions Catalyzed by Haloalkane Dehalogenases Westerbeek, A Szymanski, W Wijma, HJ, Marrink, SJ, Feringa, BL, Janssen, DB Adv. Synth. Catal. 353, 931-944 |
High-performance prediction of functional residues in proteins with machine learning and computed input features. Somarowthu S, Yang H, Hildebrand DG, Ondrechen MJ. Biopolymers. 2011 Jun;95(6):390-400. |
Structure-Function Relationship of Cytoplasmic and Nuclear IkB Proteins: An In Silico Analysis Manavalan B, Basith S, Choi YM, Lee G, Choi S PLoS One. 2010 Dec 23;5(12):e15782 |
A series of PDB related databases for everyday needs Joosten RP, te Beek TA, Krieger E, Hekkelman ML, Hooft RW, Schneider R, Sander C, Vriend G Nucleic Acids Res. 2011 Jan;39(Database issue):D411-9 |
Modulation of human ether a gogo related channels by CASQ2 contributes to etiology of catecholaminergic polymorphic ventricular tachycardia (CPVT). Eckey K, Strutz-Seebohm N, Katz G, Fuhrmann G, Henrion U, Pott L, Linke WA, Arad M, Lang F, Seebohm G. Cell Physiol Biochem. 2010;26(4-5):503-12 |
HFE gene mutations in patients with primary iron overload: is there a significant improvement in molecular diagnosis yield with HFE sequencing? Santos PC, Pereira AC, Cancado RD, Schettert IT, Sobreira TJ, Oliveira PS, Hirata RD, Hirata MH, Figueiredo MS, Chiattone CS, Krieger JE, Guerra-Shinohara EM Blood Cells Mol Dis. 2010 Dec 15;45(4):302-7 |
DFG-in and DFG-out homology models of TrkB kinase receptor: Induced-fit and ensemble docking Podlipnik C, Tutino F, Bernardi A, Seneci P J Mol Graph Model. 2010 Oct 7 |
Insights into Egg Coat Assembly and Egg-Sperm Interaction from the X-Ray Structure of Full-Length ZP3 Han L, Monne M, Okumura H, Schwend T, Cherry AL, Flot D, Matsuda T, Jovine L Cell. 2010 Oct 20 |
Residues at the tip of the pore loop of NR3B-containing NMDA receptors determine Ca2+ permeability and Mg2+ block. Cavara NA, Orth A, Hicking G, Seebohm G, Hollmann M. BMC Neurosci. 2010 Oct 19;11:133. |
Engineering of an enantioselective tyrosine aminomutase by mutation of a single active site residue in phenylalanine aminomutase Wu B, Szymaski W, Wijma HJ, Crismaru CG, de Wildeman S, Poelarends GJ, Feringa BL, Janssen DB Chem Commun (Camb). 2010 Nov 21;46(43):8157-9 |
Two-dimensional heteronuclear saturation transfer difference NMR reveals detailed integrin avb6 protein-peptide interactions Wagstaff JL, Vallath S, Marshall JF, Williamson RA, Howard MJ Chem Commun (Camb). 2010 Oct 28;46(40):7533-5 |
NMR structure of the human prion protein with the pathological Q212P mutation reveals unique structural features Ilc G, Giachin G, Jaremko M, Jaremko L, Benetti F, Plavec J, Zhukov I, Legname G PLoS One. 2010 Jul 22;5(7):e11715 |
The {alpha}-galactosidase type A gene aglA from Aspergillus niger encodes a fully functional {alpha}-N-acetylgalactosaminidase Kulik N, Weignerova L, Filipi T, Pompach P, Novak P, Mrazek H, Slamova K, Bezouska K, Kren V, Ettrich R Glycobiology. 2010 Nov;20(11):1410-9 |
In silico prediction of the 3D structure of trimeric asialoglycoprotein receptor bound to triantennary oligosaccharide Ramadugu SK, Chung YH, Fuentes EJ, Rice KG, Margulis CJ J Am Chem Soc. 2010 Jul 7;132(26):9087-95 |
Monte Carlo-based rigid body modelling of large protein complexes against small angle scattering data Meesters C, Pairet B, Rabenhorst A, Decker H, Jaenicke E Comput Biol Chem. 2010 Jun;34(3):158-64 |
A Tale of Two Acids: When Arginine Is a More Appropriate Acid than H(3)O(+) Silva PJ, Schulz C, Jahn D, Jahn M, Ramos MJ J Phys Chem B. 2010 Jun 16 |
Systematic structure-function analysis of androgen receptor Leu701 mutants explains the properties of the prostate cancer mutant L701H van de Wijngaart DJ, Molier M, Lusher SJ, Hersmus R, Jenster G, Trapman J, Dubbink HJ J Biol Chem. 2010 Feb 12;285(7):5097-105 |
Factor VIII-eGFP fusion proteins with preserved functional activity for the analysis of the early secretory pathway of factor VIII. Heinz S, Schuettrumpf J, Simpson JC, Pepperkok R, Nicolaes GA, Abriss D, Milanov P, Roth S, Seifried E, Tonn T. Thromb Haemost. 2009 Nov;102(5):925-35. doi: 10.1160/TH08-12-0807. |
Homology modelling and spectroscopy, a never-ending love story Venselaar H, Joosten RP, Vroling B, Baakman CA, Hekkelman ML, Krieger E, Vriend G Eur Biophys J. 2010 Mar;39(4):551-63 |
Molecular dynamics analysis of the wild type and dF508 mutant structures of the human CFTR-nucleotide binding domain 1 Bisignano P, Moran O Biochimie. 2010 Jan;92(1):51-57 |
Folding defects in P-type ATP 8B1 associated with hereditary cholestasis are ameliorated by 4-phenylbutyrate van der Velden LM, Stapelbroek JM, Krieger E, van den Berghe PV, Berger R, Verhulst PM, Holthuis JC, Houwen RH, Klomp LW, van de Graaf SF Hepatology. 2010 Jan;51(1):286-96 |
![]() Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K Proteins. 2009;77 Suppl 9:114-22 The journal cover shows how the knowledge-based potentials in the YASARA force field cover the various dihedral angles of an arginine residue. |
![]() Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ and Vriend G J. Appl. Cryst. (2009). 42, 376-384 Journal cover made with YASARA. |
Challenging a paradigm: theoretical calculations of the protonation state of the Cys25-His159 catalytic diad in free papain Shokhen M, Khazanov N, Albeck A. Proteins. 2009 Dec;77(4):916-26 |
Reduced expression of ATP7B affected by Wilson disease-causing mutations is rescued by pharmacological folding chaperones 4-phenylbutyrate and curcumin van den Berghe PV, Stapelbroek JM, Krieger E, de Bie P, van de Graaf SF, de Groot RE, van Beurden E, Spijker E, Houwen RH, Berger R, Klomp LW Hepatology. 2009 Dec;50(6):1783-95 |
Antibacterial activity of six novel peptides from Tityus discrepans scorpion venom. A fluorescent probe study of microbial membrane Na+ permeability changes Diaz P, D'Suze G, Salazar V, Sevcik C, Shannon JD, Sherman NE, Fox JW. Toxicon. 2009 Nov;54(6):802-17 |
Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity Demon D, Van Damme P, Vanden Berghe T, Deceuninck A, Van Durme J, Verspurten J, Helsens K, Impens F, Wejda M, Schymkowitz J, Rousseau F, Madder A, Vandekerckhove J, Declercq W, Gevaert K, Vandenabeele P Mol Cell Proteomics. 2009 Sep 16 |
Homology modelling and spectroscopy, a never-ending love story Venselaar H, Joosten RP, Vroling B, Baakman CA, Hekkelman ML, Krieger E, Vriend G Eur Biophys J. 2009 Aug 29 |
Molecular Dynamics Analysis Of The Wild Type And dF508 Mutant Structures Of The Human CFTR-Nucleotide Binding Domain 1 Bisignano P and Moran O Biochemie (2009) in press |
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Accurate prediction of DnaK-peptide binding via homology modelling and experimental data Van Durme J, Maurer-Stroh S, Gallardo R, Wilkinson H, Rousseau F, Schymkowitz J PLoS Comput Biol. 2009 Aug;5(8):e1000475 |
Long QT syndrome-associated mutations in the voltage sensor of I(Ks) channels. Henrion U, Strutz-Seebohm N, Duszenko M, Lang F, Seebohm G. Cell Physiol Biochem. 2009;24(1-2):11-6 |
Structure of the tyrosine-sulfated C5a receptor N terminus in complex with chemotaxis inhibitory protein of Staphylococcus aureus Ippel JH, de Haas CJ, Bunschoten A, van Strijp JA, Kruijtzer JA, Liskamp RM, Kemmink J J Biol Chem. 2009 May 1;284(18):12363-72 |
Influence of dihydropyrimidine dehydrogenase gene (DPYD) coding sequence variants on the development of fluoropyrimidine-related toxicity in patients with high-grade toxicity and patients with excellent tolerance of fluoropyrimidine-based chemotherapy. Kleibl Z, Fidlerova J, Kleiblova P, Kormunda S, Bilek M, Bouskova K, Sevcik J, Novotny J. Neoplasma. 2009;56(4):303-16. |
Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites Maurer-Stroh S, Ma J, Lee RT, Sirota FL, Eisenhaber F Biol Direct. 2009 May 20;4(1):18 |
A single residue influences the reaction mechanism of ammonia lyases and mutases Bartsch S and Bornscheuer UT Angew Chem Int Ed Engl. 2009;48(18):3362-5 |
Structure of the tyrosine-sulfated C5a receptor N terminus in complex with chemotaxis inhibitory protein of Staphylococcus aureus Ippel JH, de Haas CJ, Bunschoten A, van Strijp JA, Kruijtzer JA, Liskamp RM, Kemmink J J Biol Chem. 2009 May 1;284(18):12363-72 An NMR structure determined with the help of YASARA, PDB ID 2K3U |
Protein sequences encode safeguards against aggregation Reumers J, Maurer-Stroh S, Schymkowitz J, Rousseau F Hum Mutat. 2009 Mar;30(3):431-7 |
Brominated phenols as auxin-like molecules Spaepena S, Van Durme J, Dasa F, Maurer-Stroh S, Rousseau F, Schymkowitzb J and Vanderleydena J Europ. J. of Soil Biol. 2009;45:81-87 |
Functional Role of Arginine 375 in Transmembrane Helix 6 of Multidrug Resistance Protein 4 (MRP4/ABCC4) El-Sheikh AA, van den Heuvel JJ, Krieger E, Russel FG, Koenderink JB Mol Pharmacol. 2008 Oct;74(4):964-71 |
Differential blocking effects of the acetaldehyde-derived DNA lesion N2-ethyl-2'-deoxyguanosine on transcription by multisubunit and single subunit RNA polymerases Cheng TF, Hu X, Gnatt A, Brooks PJ J Biol Chem. 2008 Oct 10;283(41):27820-8 |
Structural characterization of the alpha-hemolysin monomer from Staphylococcus aureus Meesters C, Brack A, Hellmann N, Decker H Proteins. 2008 Sep 17;75(1):118-126 |
The crystal structure of the platelet activator aggretin reveals a novel (alphabeta)2 dimeric structure Hooley E, Papagrigoriou E, Navdaev A, Pandey AV, Clemetson JM, Clemetson KJ, Emsley J Biochemistry. 2008 Jul 29;47(30):7831-7 |
A Software Library for Monte Carlo-Based Rigid Body Modelling Against Small Angle Scattering Data Meesters C From Computational Biophysics to Systems Biology (CBSB08) NIC Series, Vol. 40 |
Identification of surface epitopes of human coagulation factor Va which are important for interaction with activated protein C and heparin Segers K, Dahlback B, Rosing J, Nicolaes GA J Biol Chem. 2008 Jun 2 |
Complete inversion of enantioselectivity towards acetylated tertiary alcohols by a double mutant of a Bacillus subtilis esterase Bartsch S, Kourist R, Bornscheuer UT Angew Chem Int Ed Engl. 2008;47(8):1508-11 |
![]() Kemna EHJM, Tjalsma H, Willems HL, Swinkels DW Haematologica, 93(1):90-97. Journal cover made with YASARA: |
A three-dimensional model of mammalian tyrosinase active site accounting for loss of function mutations Schweikardt T, Olivares C, Solano F, Jaenicke E, Garcia-Borron JC, Decker H Pigment Cell Res. 2007 Oct;20(5):394-401 |
MYO15A (DFNB3) mutations in Turkish hearing loss families and functional modeling of a novel motor domain mutation Kalay E, Uzumcu A, Krieger E, Caylan R, Uyguner O, Ulubil-Emiroglu M, Erdol H, Kayserili H, Hafiz G, Baserer N, Heister AJ, Hennies HC, Nurnberg P, Basaran S, Brunner HG, Cremers CW, Karaguzel A, Wollnik B, Kremer H Am J Med Genet A. 2007 Oct 15;143(20):2382-9 |
Structural diversity in twin-arginine signal peptide-binding proteins Maillard J, Spronk CA, Buchanan G, Lyall V, Richardson DJ, Palmer T, Vuister GW, Sargent F Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15641-6 An NMR structure determined with the help of YASARA, PDB ID 2JSX |
Screening of the active site from water by the incoming ligand triggers catalysis and inhibition in serine proteases Shokhen M, Khazanov N, Albeck A Proteins. 2007 Oct 2 |
Similar enzyme activation and catalysis in hemocyanins and tyrosinases Decker H, Schweikardt T, Nillius D, Salzbrunn U, Jaenicke E, Tuczek F Gene. 2007 Aug 15;398(1-2):183-91 |
Clinical, structural and functional implications of mutations and polymorphisms in human NADPH P450 oxidoreductase Fluck CE, Nicolo C, Pandey AV Fundam Clin Pharmacol. 2007 Aug;21(4):399-410 |
The cytochrome P450 aromatase lacking exon 5 is associated with a phenotype of nonclassic aromatase deficiency and is also present in normal human steroidogenic tissues Pepe CM, Saraco NI, Baquedano MS, Guercio G, Vaiani E, Marino R, Pandey AV, Fluck CE, Rivarola MA, Belgorosky A Clin Endocrinol (Oxf). 2007 Jul 2 |
Amino acids in the second transmembrane helix of the Lhca4 subunit are important for formation of stable heterodimeric light-harvesting complex LHCI-730 Corbet D, Schweikardt T, Paulsen H, Schmid VH J Mol Biol. 2007 Jun 29;370(1):170-82 |
Modulation of human cyp19a1 activity by mutant nadph p450 oxidoreductase Pandey AV, Kempna P, Hofer G, Mullis PE, Fluck CE Mol Endocrinol. 2007 Jun 26 |
MPP1 links the Usher protein network and the Crumbs protein complex in the retina Gosens I, van Wijk E, Kersten FF, Krieger E, van der Zwaag B, Marker T, Letteboer SJ, Dusseljee S, Peters T, Spierenburg HA, Punte IM, Wolfrum U, Cremers FP, Kremer H, Roepman R Hum Mol Genet. 2007 Jun 21 |
Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies Ettrich R, Kopecky V Jr, Hofbauerova K, Baumruk V, Novak P, Pompach P, Man P, Plihal O, Kuty M, Kulik N, Sklenar J, Ryslava H, Kren V, Bezouska K BMC Struct Biol. 2007 May 17;7:32 |
PSA/KLK3 AREI promoter polymorphism alters androgen receptor binding and is associated with prostate cancer susceptibility Lai J, Kedda MA, Hinze K, Smith RL, Yaxley J, Spurdle AB, Morris CP, Harris J, Clements JA Carcinogenesis. 2006 Dec 13 |
Influence of modulated structural dynamics on the kinetics of alpha-chymotrypsin catalysis. Insights through chemical glycosylation, molecular dynamics and domain motion analysis Sola RJ, Griebenow K FEBS J. 2006 Dec;273(23):5303-19 |
The human Vps29 retromer component is a metallo-phosphoesterase for a cation-independent mannose 6-phosphate receptor substrate peptide Damen E, Krieger E, Nielsen JE, Eygensteyn J, van Leeuwen JE Biochem J. 2006 Sep 15;398(3):399-409 |
Structure-function analysis of the coxsackievirus protein 3A: identification of residues important for dimerization, viral RNA replication, and transport inhibition Wessels E, Notebaart RA, Duijsings D, Lanke K, Vergeer B, Melchers WJ, van Kuppeveld FJ J Biol Chem. 2006 281(38):28232-43 |
The first crystal structure of tyrosinase: all questions answered? Decker H, Schweikardt T, Tuczek F Angew Chem Int Ed Engl. 2006 Jul 10;45(28):4546-50 |
Arrestin interaction with rhodopsin: conceptual models Modzelewska A, Filipek S, Palczewski K, Park PS Cell Biochem Biophys. 2006;46(1):1-15 |
Structural models of the snake venom factor V activators from Daboia russelli and Daboia lebetina Segers K, Rosing J, Nicolaes GA Proteins. 2006 Sep 1;64(4):968-84 |
![]() Van Durme J, Horn F, Costagliola S, Vriend G, Vassart G Mol Endocrinol. 2006 Sep;20(9):2247-55 Journal cover partly made with YASARA: |
Completely buried, non-ion-paired glutamic acid contributes favorably to the conformational stability of pyrrolidone carboxyl peptidases from hyperthermophiles. Kaushik JK, Iimura S, Ogasahara K, Yamagata Y, Segawa S, Yutani K Biochemistry. 2006 Jun 13;45(23):7100-12. |
![]() Harjes E, Harjes S, Wohlgemuth S, Muller KH, Krieger E, Herrmann C, Bayer P. Structure 2006 May;14(5):881-8 An NMR structure determined with the help of YASARA, PDB ID 2FNF. Journal cover made with YASARA: |
Fast empirical pK(a) prediction by Ewald summation. Krieger E, Nielsen JE, Spronk CA, Vriend G. J Mol Graph Model. 2006 Apr 25 |
The presence of multiple and differentially regulated interleukin-12p40 genes in bony fishes signifies an expansion of the vertebrate heterodimeric cytokine family. Huising MO, van Schijndel JE, Kruiswijk CP, Nabuurs SB, Savelkoul HF, Flik G, Verburg-van Kemenade BM Mol Immunol. 2006 Apr;43(10):1519-33 |
Repulsive separation of the cytoplasmic ends of transmembrane helices 3 and 6 is linked to receptor activation in a novel thyrotropin receptor mutant (M626I). Ringkananont U, Van Durme J, Montanelli L, Ugrasbul F, Yu YM, Weiss RE, Refetoff S, Grasberger H. Mol Endocrinol. 2006 Apr;20(4):893-903 |
ZNF674: A New Kruppel-Associated Box-Containing Zinc-Finger Gene Involved in Nonsyndromic X-Linked Mental Retardation. Lugtenberg D, Yntema HG, Banning MJ, Oudakker AR, Firth HV, Willatt L, Raynaud M, Kleefstra T, Fryns JP, Ropers HH, Chelly J, Moraine C, Gecz J, Reeuwijk J, Nabuurs SB, de Vries BB, Hamel BC, de Brouwer AP, Bokhoven H Am J Hum Genet. 2006 Feb;78(2):265-78 |
A novel D458V mutation in the SANS PDZ binding motif causes atypical Usher syndrome. Kalay E, de Brouwer AP, Caylan R, Nabuurs SB, Wollnik B, Karaguzel A, Heister JG, Erdol H, Cremers FP, Cremers CW, Brunner HG, Kremer H. J Mol Med. 2005 Dec;83(12):1025-32. |
A novel GCAP1 missense mutation (L151F) in a large family with autosomal dominant cone-rod dystrophy (adCORD) Sokal I, Dupps WJ, Grassi MA, Brown J Jr, Affatigato LM, Roychowdhury N, Yang L, Filipek S, Palczewski K, Stone EM, Baehr W Invest Ophthalmol Vis Sci. 2005 Apr;46(4):1124-32 |
Interaction of nephrocystin-4 and RPGRIP1 is disrupted by nephronophthisis or Leber congenital amaurosis-associated mutations. Roepman R, Letteboer SJ, Arts HH, van Beersum SE, Lu X, Krieger E, Ferreira PA, Cremers FP. Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18520-5 |
A novel D458V mutation in the SANS PDZ binding motif causes atypical Usher syndrome. Kalay E, de Brouwer AP, Caylan R, Nabuurs SB, Wollnik B, Karaguzel A, Heister JG, Erdol H, Cremers FP, Cremers CW, Brunner HG, Kremer H. J Mol Med. 2005 Dec;83(12):1025-32 |
Definition of a new information-based per-residue quality parameter. Nabuurs SB, Krieger E, Spronk CA, Nederveen AJ, Vriend G, Vuister GW. J Biomol NMR. 2005 Oct;33(2):123-34. |
Presence and absence of FSH receptor mutations provide some insights to spontaneous ovarian hyperstimulation syndrome physiopathology. De Leener A, Montanelli L, Van Durme J, Chae H, Smits G, Vassart G, Costagliola S. J Clin Endocrinol Metab. 2005 Nov 8; |
![]() Qiu LY, Krieger E, Schaftenaar G, Swarts HG, Willems PH, De Pont JJ, Koenderink JB. J Biol Chem. 2005 Sep 16;280(37):32349-55 Journal cover made with YASARA: |
MPP5 recruits MPP4 to the CRB1 complex in photoreceptors. Kantardzhieva A, Gosens I, Alexeeva S, Punte IM, Versteeg I, Krieger E, Neefjes-Mol CA, den Hollander AI, Letteboer SJ, Klooster J, Cremers FP, Roepman R, Wijnholds J. Invest Ophthalmol Vis Sci. 2005 Jun;46(6):2192-201 |
Asn792 Participates in the Hydrogen Bond Network Around the K+-binding Pocket of Gastric H,K-ATPase. Swarts HG, Koenderink JB, Willems PH, Krieger E, De Pont JJ. J Biol Chem. 2005 Mar 25;280(12):11488-94 |
A Proline-Rich Region in the Coxsackievirus 3A Protein Is Required for the Protein To Inhibit Endoplasmic Reticulum-to-Golgi Transport. Wessels E, Duijsings D, Notebaart RA, Melchers WJ, van Kuppeveld FJ. J Virol. 2005 Apr;79(8):5163-73 |
Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials. Wiederstein M, Sippl MJ. J Mol Biol. 2005 Feb 4;345(5):1199-212 |
Validation of protein structures derived by NMR spectroscopy. Spronk CA, Nabuurs SB, Krieger E, Vriend G, Vuister GW. Progress in NMR spectroscopy. 2004 45:315-337. |
Making optimal use of empirical energy functions: Force-field parameterization in crystal space. Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G. Proteins. 2004 57(4):678-683 |
![]() Costagliola S, Bonomi M, Morgenthaler NG, Van Durme J, Panneels V, Refetoff S, Vassart G. Mol Endocrinol. 2004 18(12):3020-34 Journal cover made with YASARA: |
OmpT: Molecular Dynamics Simulations of an Outer Membrane Enzyme. Baaden M, Sansom MS. Biophys J. 2004 87(5):2942-53 |
Identification of the MMRN1 binding region within the C2 domain of human factor V. Jeimy SB, Woram RA, Fuller N, Quinn-Allen MA, Nicolaes GA, Dahlback B, Kane WH, Hayward CP. J Biol Chem. 2004 279(49):51466-71 |
DRESS: a database of REfined solution NMR structures. Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF, Bonvin AM, Vuister GW, Vriend G, Spronk CA. Proteins. 2004 55(3):483-6. |
Identification and molecular modelling of a mutation in the motor head domain of myosin VIIA in a family with autosomal dominant hearing impairment (DFNA11). Luijendijk MW, Van Wijk E, Bischoff AM, Krieger E, Huygen PL, Pennings RJ, Brunner HG, Cremers CW, Cremers FP, Kremer H. Hum Genet. 2004 115(2):149-56. |
A conformation-specific interhelical salt bridge in the K+ binding site of gastric H,K-ATPase. Koenderink JB, Swarts HG, Willems PH, Krieger E, De Pont JJ. J Biol Chem. 2004 279(16):16417-24. |
A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations. Krieger E, Geretti E, Brandner B, Goger B, Wells TN, Kungl AJ. Proteins. 2004 54(4):768-75. |
A mutation in the gamma actin 1 (ACTG1) gene causes autosomal dominant hearing loss (DFNA20/26). van Wijk E, Krieger E, Kemperman MH, De Leenheer EM, Huygen PL, Cremers CW, Cremers FP, Kremer H. J Med Genet. 2003 40(12):879-84. |
Fluorescence analysis of the Hansenula polymorpha peroxisomal targeting signal-1 receptor, Pex5p. Boteva R, Koek A, Visser NV, Visser AJ, Krieger E, Zlateva T, Veenhuis M, van der Klei I. Eur J Biochem. 2003 270(21):4332-8. |
DJ-1( PARK7), a novel gene for autosomal recessive, early onset parkinsonism. Bonifati V, Rizzu P, Squitieri F, Krieger E, Vanacore N, van Swieten JC, Brice A, van Duijn CM, Oostra B, Meco G, Heutink P. Neurol Sci. 2003 24(3):159-60. |
Quantitative Evaluation of Experimental NMR Restraints. Nabuurs SB, Spronk CA, Krieger E, Maassen H, Vriend G, Vuister GW. J Am Chem Soc. 2003 125(39):12026-12034. |
The precision of NMR structure ensembles revisited. Spronk CA, Nabuurs SB, Bonvin AM, Krieger E, Vuister GW, Vriend G. J Biomol NMR. 2003 25(3):225-34. |
Homology modeling. Krieger E, Nabuurs SB, Vriend G. Methods Biochem Anal. 2003;44:509-23. |
Mutations in the DJ-1 gene associated with autosomal recessive early-onset parkinsonism. Bonifati V, Rizzu P, van Baren MJ, Schaap O, Breedveld GJ, Krieger E, Dekker MC, Squitieri F, Ibanez P, Joosse M, van Dongen JW, Vanacore N, van Swieten JC, Brice A, Meco G, van Duijn CM, Oostra BA, Heutink P. Science. 2003 299(5604):256-9 |
A mutation in the fibroblast growth factor 14 gene is associated with autosomal dominant cerebellar ataxia. van Swieten JC, Brusse E, de Graaf BM, Krieger E, van de Graaf R, de Koning I, Maat-Kievit A, Leegwater P, Dooijes D, Oostra BA, Heutink P. Am J Hum Genet. 2003 72(4):1078. |
Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field. Krieger E, Koraimann G, Vriend G. Proteins. 2002 47(3):393-402. |
Gain-of-function mutation in ADULT syndrome reveals the presence of a second transactivation domain in p63. Duijf PH, Vanmolkot KR, Propping P, Friedl W, Krieger E, McKeon F, Dotsch V, Brunner HG, van Bokhoven H. Hum Mol Genet. 2002 11(7):799-804. |
Identification of different binding sites in the dendritic cell-specific receptor DC-SIGN for intercellular adhesion molecule 3 and HIV-1. Geijtenbeek TB, van Duijnhoven GC, van Vliet SJ, Krieger E, Vriend G, Figdor CG, van Kooyk Y. J Biol Chem. 2002 277(13):11314-20. |
Models@Home: distributed computing in bioinformatics using a screensaver based approach. Krieger E, Vriend G. Bioinformatics. 2002 18(2):315-8. |