User:Wayne Decatur/Molecular modeling tools
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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] | ||
| - | * YASARA | + | * [http://www.yasara.org/ YASARA] - Yet Another Scientific Artificial Reality Application) is an interactive real- time molecular dynamics program. Also YASARA Structure features a complete homology modeling module that fully automatically takes all the steps from an amino acid sequence to a refined high-resolution model using a CASP approved protocol. |
* UCSF Chimera | * UCSF Chimera | ||
* Ascalaph Designer | * Ascalaph Designer | ||
* [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. | ||
Current revision
- Schrödinger Molecular Modeling Platform - Small Molecule and Macromolecule Modeling and Simulations.
- Accelrys Discovery Studio - Accelrys and Symyx merged effective July 1, 2010.
- Rosetta Software Suite includes Modeling abilities and as a related package, there is PyRosetta - an interactive Python-based interface for Interactive Molecular Modeling.
- TINKER - Software Tools for Molecular Design.
- 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. 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 SWISS-MODEL.
- Modeller
- YASARA - Yet Another Scientific Artificial Reality Application) is an interactive real- time molecular dynamics program. Also YASARA Structure features a complete homology modeling module that fully automatically takes all the steps from an amino acid sequence to a refined high-resolution model using a CASP approved protocol.
- UCSF Chimera
- Ascalaph Designer
- Packmol for molecular dynamic simulations with pdb and xyz files (as described by The Open Science Project)
- 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 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 'How to run Interactive Molecular Dynamics' and '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
- 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
- Symyx JDraw Applet - as they describe it: "In addition to accessing the no-fee Symyx Draw desktop application, students, teachers, and researchers working in a non-commercial setting can now access capabilities for rapidly drawing chemical structures and chemically intelligent queries in Web applications–capabilities built on industry-leading Symyx chemistry representation technology." Symyx Draw is similar to ISIS/Draw and has advanced features.
- The ISU CheMagic USM O=CHem Virtual Molecular Model Kit, as detailed 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 ACD/Labs’ ChemSketch.
- Jmol on its own now has some ability to be directly used as a chemistry modeling kit for small molecules and there is a 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 here.
- chemCanvas, an open source chemical diagram editor for making models of small molecules. Site about it is here.
- ChemAxon's Marvin Sketch and ChemDoodle has the ability to draw reactions and structures. And you can put chemistry on the web with Metamolecular's ChemWriter.
- ChemTube3D isn't for modeling but contains interactive 3D animations and structures of molecular reactions basic to chemistry.
- The Jmol Interface by Mike Evans at University of Illinois has a useful page for drawing arrows and making chemical structures in Jmol.
- iView - an interactive WebGL visualizer of protein-ligand complexes
- PrePPI: database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.
See Also
- Homology model
- My persornal page on Homology Modeling
- Molecular modeling and visualization software
- 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.
