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.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]'. | * [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 Python-based 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. | |||
==Related== | ==Related== | ||
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* [http://chemcanvas.sourceforge.net/chemWin.html chemCanvas], an open source chemical diagram editor for making models of small molecules. Site about it is [http://chemcanvas.sourceforge.net/ here]. | * [http://chemcanvas.sourceforge.net/chemWin.html chemCanvas], an open source chemical diagram editor for making models of small molecules. Site about it is [http://chemcanvas.sourceforge.net/ here]. | ||
* [http://www.chemaxon.com/products/marvin/ ChemAxon's Marvin Sketch] and [http://www.chemdoodle.com/ ChemDoodle] has the ability to draw reactions and structures. And you can put chemistry on the web with [http://metamolecular.com/software Metamolecular's ChemWriter]. | * [http://www.chemaxon.com/products/marvin/ ChemAxon's Marvin Sketch] and [http://www.chemdoodle.com/ ChemDoodle] has the ability to draw reactions and structures. And you can put chemistry on the web with [http://metamolecular.com/software Metamolecular's ChemWriter]. | ||
* [http://www.chemtube3d.com/Diels-Alder%20-%20Stereochemistry%20of%20the%20diene%20%28cis-trans%29.html ChemTube3D] isn't for modeling but contains interactive 3D animations and structures of molecular reactions basic to chemistry. | * [http://www.chemtube3d.com/Diels-Alder%20-%20Stereochemistry%20of%20the%20diene%20%28cis-trans%29.html ChemTube3D] isn't for modeling but contains interactive 3D animations and structures of molecular reactions basic to chemistry. | ||
* [http://butane.chem.illinois.edu/jsmoore/Experimental/mpjmols/JManip.aspx The Jmol Interface by Mike Evans at University of Illinois] has a useful page for drawing arrows and making chemical structures in Jmol. | |||
* [http://istar.cse.cuhk.edu.hk/iview/ iView] - an interactive WebGL visualizer of protein-ligand complexes | |||
* [https://bhapp.c2b2.columbia.edu/PrePPI/ PrePPI]: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human. | |||
==See Also== | ==See Also== | ||
