YASARA in press

Please also notify us in case you use YASARA yourself and have a paper to be added here, which mentions YASARA.

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

Hepcidin: from discovery to differential diagnosis 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

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

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

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

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

GRIS: Glycoprotein-Hormone Receptor Information System. 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.

GTP-Ras Disrupts the Intramolecular Complex of C1 and RA Domains of Nore1. Harjes E, Harjes S, Wohlgemuth S, Muller KH , Krieger E, Herrmann C, Bayer P. Structure. 2006 May;14(5):881-8. 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;

Reconstruction of the Complete Ouabain-binding Pocket of Na,K-ATPase in Gastric H,K-ATPase by Substitution of Only Seven Amino Acids. 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

Delineation of the discontinuous-conformational epitope of a monoclonal antibody displaying full in vitro and in vivo thyrotropin activity. 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.