User:Wayne Decatur/Molecular modeling tools: Difference between revisions

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* [http://www.ime.unicamp.br/~martinez/packmol/ Packmol] for molecular dynamic simulations with pdb and xyz files (as described by [http://www.openscience.org/blog/?p=399 The Open Science Project])

* [http://www.ks.uiuc.edu/Research/vmd/ VMD or Visual Molecular Dynamics] is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting and has an extension called [http://www.scs.illinois.edu/schulten/multiseq/ MultiSeq], which is a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids with a special emphasis is placed on analyzing the data within the framework of evolutionary biology. VMD and Multiseq have many tutorials such as '[http://www.ks.uiuc.edu/Research/vmd/imd/tutorial/ How to run Interactive Molecular Dynamics]' and '[http://www.scs.illinois.edu/schulten/tutorials/index.html Evolution of Translation: Ribosome]'.

* A modern, open library for the analysis of molecular dynamics trajectories http://www.mdtraj.org https://github.com/mdtraj/mdtraj

* [http://sysimm.ifrec.osaka-u.ac.jp/OSCAR/ OSCAR (Optimized Side Chain Atomic eneRgy )] performs side-chain modeling based on orientation-dependent energy functions and a rigid rotamer model. The settings are appropriate for protein loop selection, especially for decoys without extensive structural refinement.

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 * [http://www.ime.unicamp.br/~martinez/packmol/  Packmol] for molecular dynamic simulations with pdb and xyz files (as described by [http://www.openscience.org/blog/?p=399 The Open Science Project])
 * [http://www.ks.uiuc.edu/Research/vmd/ VMD or Visual Molecular Dynamics] is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting and has an extension called [http://www.scs.illinois.edu/schulten/multiseq/ MultiSeq], which is a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids with a special emphasis is placed on analyzing the data within the framework of evolutionary biology. VMD and Multiseq have many tutorials such as '[http://www.ks.uiuc.edu/Research/vmd/imd/tutorial/ How to run Interactive Molecular Dynamics]' and '[http://www.scs.illinois.edu/schulten/tutorials/index.html Evolution of Translation: Ribosome]'.
+* A modern, open library for the analysis of molecular dynamics trajectories http://www.mdtraj.org https://github.com/mdtraj/mdtraj
 * [http://sysimm.ifrec.osaka-u.ac.jp/OSCAR/ OSCAR (Optimized Side Chain Atomic eneRgy )] performs side-chain modeling based on orientation-dependent energy functions and a rigid rotamer model. The settings are appropriate for protein loop selection, especially for decoys without extensive structural refinement.