User:Wayne Decatur/Molecular modeling tools: Difference between revisions
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* [http://dasher.wustl.edu/tinker/ TINKER] - Software Tools for Molecular Design. | * [http://dasher.wustl.edu/tinker/ TINKER] - Software Tools for Molecular Design. | ||
* [http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase: Database of Comparative Protein Structure Models] also allows users to calculate comparative models on demand. | * [http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase: Database of Comparative Protein Structure Models] also allows users to calculate comparative models on demand. | ||
* [[PyMOL]] is primarily a molecular viewer but allows some changes to be made. [http://www.pymol.org/news | * [[PyMOL]] is primarily a molecular viewer but allows some changes to be made. [http://www.pymol.org/news Schrödinger took over development of PyMol] after Warren DeLano's unexpected passing on November 3, 2009 | ||
* [[Swiss-PDBViewer = DeepView]], a powerful and popular free modeling package (not open-source). Has an interface linked to [http://swissmodel.expasy.org/ SWISS-MODEL]. | * [[Swiss-PDBViewer = DeepView]], a powerful and popular free modeling package (not open-source). Has an interface linked to [http://swissmodel.expasy.org/ SWISS-MODEL]. | ||
* [http://salilab.org/modeller/ Modeller] | * [http://salilab.org/modeller/ Modeller] | ||
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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://chemagic.com/web_molecules/script_page_large.aspx The ISU CheMagic USM O=CHem Virtual Molecular Model Kit], as detailed [http://chemagic.com/chemsketch/ here], uses CheMagic and the Jmol Virtual Molecular Model Kit & JME Molecular Editor enabling users to generate molecular models; user generated Jmol models can also be created using [http://www.acdlabs.com/products/draw_nom/ ACD/Labs’ ChemSketch]. | * [http://chemagic.com/web_molecules/script_page_large.aspx The ISU CheMagic USM O=CHem Virtual Molecular Model Kit], as detailed [http://chemagic.com/chemsketch/ here], uses CheMagic and the Jmol Virtual Molecular Model Kit & JME Molecular Editor enabling users to generate molecular models; user generated Jmol models can also be created using [http://www.acdlabs.com/products/draw_nom/ ACD/Labs’ ChemSketch]. | ||
* [http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=146 Jmol on its own now has some ability to be directly used as a chemistry modeling kit] for small molecules and there is a [http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=147 responsive docking ability for moving/sculpting small molecules relative to large molecules] in the works. * Similarly, using Jmol that can now read SMILES format, it was possible to connect Jmol to Chemene's JSDraw that will output SMILES to JMol for rendering, see the demo [http://chemapps.stolaf.edu/jmol/docs/examples-11/jsdraw/jstest.htm here]. | * [http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=146 Jmol on its own now has some ability to be directly used as a chemistry modeling kit] for small molecules and there is a [http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=147 responsive docking ability for moving/sculpting small molecules relative to large molecules] in the works. * Similarly, using Jmol that can now read SMILES format, it was possible to connect Jmol to Chemene's JSDraw that will output SMILES to JMol for rendering, see the demo [http://chemapps.stolaf.edu/jmol/docs/examples-11/jsdraw/jstest.htm 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://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.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== | ||
* [[Homology model]] | * [[Homology model]] | ||
* [[User:Wayne Decatur/Homology Modeling|My persornal page on Homology Modeling]] | |||
* [[Molecular modeling and visualization software]] | * [[Molecular modeling and visualization software]] | ||
* [http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling List of software for molecular mechanics modeling] at Wikipeida although thoroughness and how current it is are subject to question by the inclusion of RasMol which is simply a viewer with no modeling abilities that has been supplanted by better viewers such as Chime and Jmol not included on the list. | * [http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeling List of software for molecular mechanics modeling] at Wikipeida although thoroughness and how current it is are subject to question by the inclusion of RasMol which is simply a viewer with no modeling abilities that has been supplanted by better viewers such as Chime and Jmol not included on the list. | ||
