User:Wayne Decatur/Molecular modeling tools - Revision history

Wayne Decatur at 18:57, 10 July 2018

2018-07-10T18:57:37Z

← Older revision		Revision as of 18:57, 10 July 2018
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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 library for the analysis of molecular dynamics trajectories http://www.mdtraj.org https://github.com/mdtraj/mdtraj		* 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.		* [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.

Wayne Decatur at 18:56, 10 July 2018

2018-07-10T18:56:34Z

← Older revision		Revision as of 18:56, 10 July 2018
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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 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.		* [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.

Wayne Decatur at 02:36, 2 September 2014

2014-09-02T02:36:43Z

← Older revision		Revision as of 02:36, 2 September 2014
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	* [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://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		* [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==

Wayne Decatur: /* Related */

2014-02-27T14:44:50Z

← Older revision		Revision as of 14:44, 27 February 2014
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	* [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://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 ~~complex~~		* [http://istar.cse.cuhk.edu.hk/iview/ iView] - an interactive WebGL visualizer of protein-ligand complexes

	==See Also==		==See Also==

Wayne Decatur: /* Related */

2014-02-27T14:44:27Z

← Older revision		Revision as of 14:44, 27 February 2014
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	* [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://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 complex

	==See Also==		==See Also==

Wayne Decatur at 13:44, 10 October 2011

2011-10-10T13:44:19Z

← Older revision		Revision as of 13:44, 10 October 2011
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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]'.
			* [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==

Wayne Decatur: /* Related */ added Jmol interface I found useful for help drawing reaction arrows

2011-02-20T16:34:44Z

Related: added Jmol interface I found useful for help drawing reaction arrows

← Older revision		Revision as of 16:34, 20 February 2011
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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.

	==See Also==		==See Also==

Wayne Decatur at 12:33, 26 January 2011

2011-01-26T12:33:45Z

← Older revision		Revision as of 12:33, 26 January 2011
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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.

	==See Also==		==See Also==

Wayne Decatur at 00:53, 12 November 2010

2010-11-12T00:53:55Z

← Older revision		Revision as of 00:53, 12 November 2010
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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~~.html~~ Schrödinger took over development of PyMol] after Warren DeLano's unexpected passing on November 3, 2009		* [[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]

Wayne Decatur: /* See Also */

2010-11-09T18:04:57Z

← Older revision		Revision as of 18:04, 9 November 2010
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	==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.