°  Molecular dynamics °  Analyzing a molecular dynamics trajectory This macro analyzes a simulation and creates a table with energies and RMSDs from the starting structure, as well as the minimum energy structure and the time average structure with B-factors calculated from the root mean square fluctuations. If you want to do your own custom analysis, search for 'Example:'. Written by: Elmar Krieger License: GNU GPL Last modified: 2013/04/19 Download: md_analyze.mcr °  Running an accurate molecular dynamics simulation in water This macro sets up and runs a simulation. It can also continue a simulation that got interrupted. Written by: Elmar Krieger License: GNU GPL Last modified: 2013/03/25 Download: md_run.mcr °  Convert between SIM and XTC simulation trajectories This macro converts an existing MD trajectory between various formats. Supported are SIM->XTC, SIM->PDB, SIM->SIM, XTC->SIM and XTC->PDB. Written by: Elmar Krieger License: GNU GPL Last modified: 2013/03/25 Download: md_convert.mcr °  Running a steered molecular dynamics simulation in water This macro sets up and runs a steered simulation to pull a ligand from its binding site. As soon as they have been pulled apart completely and atoms start crossing periodic boundaries, the macro works no longer correctly Written by: Elmar Krieger License: GNU GPL Last modified: 2013/02/21 Download: md_runsteered.mcr °  Running a molecular dynamics simulation of a membrane protein This macro sets up and runs a membrane simulation. It scans the protein for secondary structure elements with hydrophobic surface residues, orients it accordingly and embeds it in a membrane of adjustable lipid composition. Finally a 250 ps restrained equilibration simulation is run, which ensures that the membrane can adapt to the newly embedded protein. Then the real simulation starts. Written by: Elmar Krieger License: GNU GPL Last modified: 2013/02/21 Download: md_runmembrane.mcr °  Refining a homology model by molecular dynamics simulation in water This macro runs a 500 ps simulation of a homology model using the protocol described in Proteins 57,678-683. It saves one PDB file every 25 picoseconds, including a table with force field energies to identify the best snapshot. In YASARA Structure, this table additionally contains Dihedrals, Packing1D and Packing3D checks (see the Check command). And in the Twinset, three more checks are included: PhiPsi, Backbone and Packing3. Written by: Elmar Krieger License: GNU GPL Last modified: 2013/02/21 Download: md_refine.mcr °  Analyzing the change of secondary structure in a molecular dynamics trajectory This macro analyzes a simulation and creates a table with per-residue secondary structure as well as a graphical plot Written by: Elmar Krieger License: GNU GPL Last modified: 2013/02/21 Download: md_analyzesecstr.mcr °  Analyzing a molecular dynamics trajectory per residue This macro analyzes a simulation and creates a table with average RMSFs and RMSDs from the starting structure per residue Written by: Elmar Krieger License: GNU GPL Last modified: 2013/02/21 Download: md_analyzeres.mcr °  Analyzing a molecular dynamics trajectory of multiple objects This macro analyzes a simulation and creates a table with energies and RMSDs from the starting structures for multiple objects Written by: Elmar Krieger License: GNU GPL Last modified: 2013/02/21 Download: md_analyzemul.mcr °  Play back a molecular dynamics trajectory This macro provides an interactive molecular dynamics trajectory player Written by: Elmar Krieger License: GNU GPL Last modified: 2012/08/26 Download: md_play.mcr °  Molecular modeling °  Running an energy minimization This macro runs an energy minimization of the soup without cleaning it first. Compared to the normal minimization experiment, it temporarily adds a water shell so that all force fields can be used directly, also those optimized for use with explicit solvent Written by: Elmar Krieger License: GNU GPL Last modified: 2013/02/21 Download: em_run.mcr °  Running an energy minimization This macro cleans the soup and then runs an energy minimization. Compared to the normal minimization experiment, it temporarily adds a water shell so that all force fields can be used directly, also those optimized for use with explicit solvent Written by: Elmar Krieger License: GNU GPL Last modified: 2013/02/21 Download: em_runclean.mcr °  Structure determination °  Solve an NMR structure with fixed quality This macro solves an NMR structure based on a protein sequence and a restraint file in XPLOR format. Contrary to the normal nmr_solve macro, it refines only those structures in water, that match a quality criterion, and performs an unlimited number of folding runs until the ensemble has the requested size Written by: Elmar Krieger, Sander Nabuurs, Chris Spronk License: GNU GPL Last modified: 2013/02/21 Download: nmr_solvehiqual.mcr °  Solve an NMR structure This macro solves an NMR structure based on a protein sequence and a restraint file in XPLOR format Written by: Elmar Krieger, Sander Nabuurs, Chris Spronk License: GNU GPL Last modified: 2013/02/21 Download: nmr_solve.mcr °  Refine an NMR ensemble in explicit solvent This macro refines an NMR ensemble in explicit solvent (HOH or DMSO) to increase the accuracy Written by: Elmar Krieger, Sander Nabuurs, Chris Spronk License: GNU GPL Last modified: 2013/01/25 Download: nmr_refinesolvent.mcr °  Set default parameters for NMR structure determination This macro is included by others to set default parameters Written by: Elmar Krieger, Sander Nabuurs, Chris Spronk License: GNU GPL Last modified: 2012/07/16 Download: nmr_setdefaults.mcr °  Refine an NMR ensemble in vacuo This macro refines a roughly folded structure in vacuo to create a realistic fold Written by: Elmar Krieger, Sander Nabuurs, Chris Spronk License: GNU GPL Last modified: 2012/07/16 Download: nmr_refinevacuo.mcr °  Solve an NMR structure This macro refines a single structure or structure ensemble (provided in PDB format) in vacuo & explicit solvent and finally analyzes the result Written by: Elmar Krieger, Sander Nabuurs, Chris Spronk License: GNU GPL Last modified: 2012/07/16 Download: nmr_refine.mcr °  Fold an ensemble of NMR structures This macro folds a structure from the stretched-out conformation using NMR restraints Written by: Elmar Krieger, Sander Nabuurs, Chris Spronk License: GNU GPL Last modified: 2012/07/16 Download: nmr_fold.mcr °  Analyze and merge an NMR ensemble This macro analyzes an NMR ensemble and merges the members into a single PDB file Written by: Elmar Krieger, Sander Nabuurs, Chris Spronk License: GNU GPL Last modified: 2012/07/16 Download: nmr_analyze.mcr °  Refine an NMR ensemble in explicit solvent This macro refines an NMR ensemble in explicit solvent to increase the accuracy Written by: Elmar Krieger, Sander Nabuurs, Chris Spronk License: GNU GPL Last modified: 2012/01/19 Download: nmr_refinewater.mcr °  Structure prediction °  Docking many ligands to a receptor to perform virtual screening This macro docks multiple ligands against a receptor and saves a sorted table of their binding energies, as well as the corresponding complexes Written by: Elmar Krieger License: GNU GPL Last modified: 2013/03/25 Download: dock_runscreening.mcr °  Docking a ligand to a receptor This macro predicts the structure of a ligand-receptor complex. It can also continue a docking run that got interrupted. An analysis log file is written at the end. Written by: Elmar Krieger License: GNU GPL Last modified: 2013/03/25 Download: dock_run.mcr °  Docking a ligand to a receptor locally This macro samples local ligand conformations in a user-supplied complex. An analysis log file is written at the end. Written by: Elmar Krieger License: GNU GPL Last modified: 2013/03/25 Download: dock_runlocal.mcr °  Docking a ligand to a receptor ensemble with flexible side-chains This macro predicts the structure of a ligand-receptor complex. Receptor flexibility is considered by creating a receptor ensemble with alternative high-scoring solutions of the side-chain rotamer network. An analysis log file is written at the end. The macro can also continue a docking run that got interrupted, especially if the scene has not been moved or rotated manually during the docking. Written by: Elmar Krieger License: GNU GPL Last modified: 2013/03/25 Download: dock_runensemble.mcr °  Showing the docking results interactively This macro provides an interactive player to cycle through the docking poses and clusters Written by: Elmar Krieger License: GNU GPL Last modified: 2013/03/25 Download: dock_play.mcr °  Building a homology model This macro builds a homology model using a FASTA sequence of the target, and optionally template structures and alignments. It takes some shortcuts (alignment quality, number of templates, refinement) to finish as quickly as possible Written by: Elmar Krieger License: GNU GPL Last modified: 2013/02/21 Download: hm_buildfast.mcr °  Building a homology model This macro builds a homology model using a FASTA sequence of the target, and optionally template structures and alignments Written by: Elmar Krieger License: GNU GPL Last modified: 2013/02/21 Download: hm_build.mcr