°  Molecular dynamics °  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. Written by: Elmar Krieger License: GNU GPL Last modified: 2008/02/23 Download: md_runsteered.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. If you have the Twinset installed, this table also contains PhiPsi, Backbone and Packing3 checks. Written by: Elmar Krieger License: GNU GPL Last modified: 2008/02/23 Download: md_refine.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: 2008/02/23 Download: md_run.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: 2008/02/14 Download: md_analyzemul.mcr °  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 time average structure with B-factors calculated from the root mean square fluctuations. Written by: Elmar Krieger License: GNU GPL Last modified: 2008/02/14 Download: md_analyze.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: 2008/01/31 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: 2008/01/31 Download: md_analyzeres.mcr °  Play back a molecular dynamics trajectory This macro plays back a molecular dynamics simulation, looping back to the start. Written by: Elmar Krieger License: GNU GPL Last modified: 2008/01/31 Download: md_play.mcr °  Convert between SIM and XTC simulation trajectories This macro converts an existing MD trajectory from SIM to XTC format and vice versa Written by: Elmar Krieger License: GNU GPL Last modified: 2006/10/30 Download: md_convert.mcr °  Structure determination °  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: 2008/02/23 Download: nmr_refinewater.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: 2008/02/16 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: 2008/02/16 Download: nmr_refinevacuo.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: 2008/02/16 Download: nmr_analyze.mcr °  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: 2006/12/21 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: 2006/12/21 Download: nmr_solve.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: 2006/12/21 Download: nmr_fold.mcr °  Structure prediction °  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: 2008/02/23 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: 2008/02/14 Download: dock_runlocal.mcr °  Showing the docking results interactively This macro cycles through the results of the various docking runs, and then shows the best complex in each cluster Written by: Elmar Krieger License: GNU GPL Last modified: 2007/11/25 Download: dock_play.mcr