Difference between revisions of "Knowledgebase:Chemical Molecular Modelling Programs"
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:<p>FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information. FTDock implements the Fourier correlation algorithm of Katchalski-Katzir and coworkers plus an electrostatics function amenable to Fourier correlation that was developed in this laboratory.</p> | :<p>FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information. FTDock implements the Fourier correlation algorithm of Katchalski-Katzir and coworkers plus an electrostatics function amenable to Fourier correlation that was developed in this laboratory.</p> | ||
| − | *[http://www.mdli.com/ | + | *[http://www.mdli.com/ Symix - PDB software] |
:<p>Chime allows you to view PDB (protein data base ) files from within your browser. Versions available for both the Windows and Mac platforms. Need to login to download</p> | :<p>Chime allows you to view PDB (protein data base ) files from within your browser. Versions available for both the Windows and Mac platforms. Need to login to download</p> | ||
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:<p>A web based Dynamical systems laboratory where the scenes were built with Povray.</p> | :<p>A web based Dynamical systems laboratory where the scenes were built with Povray.</p> | ||
| − | *[http:// | + | *[http://www.ccp14.ac.uk/ccp/web-mirrors/garlic/garlic/ Garlic Home Page] |
:<p>Garlic, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, linux, free software download, open source software.</p> | :<p>Garlic, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, linux, free software download, open source software.</p> | ||
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:<p>Convert Mol/BobScript output to POV-Ray and Raster3D format. Gl_render is a front-end to MolScript / BobScript, POV-Ray and Raster3D.</p> | :<p>Convert Mol/BobScript output to POV-Ray and Raster3D format. Gl_render is a front-end to MolScript / BobScript, POV-Ray and Raster3D.</p> | ||
| − | *[http:// | + | *[http://sourceforge.net/projects/joelib/ JOELib] |
:<p>JOELib is a platform independent open source computational chemistry package written in Java with output support for POV-Ray..</p> | :<p>JOELib is a platform independent open source computational chemistry package written in Java with output support for POV-Ray..</p> | ||
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:<p>mm2pov is a program which converts a MacroModel data file into a Persistence of Vision blob object. This allows you to ray-trace some really pretty pictures of your favourite molecules...</p> | :<p>mm2pov is a program which converts a MacroModel data file into a Persistence of Vision blob object. This allows you to ray-trace some really pretty pictures of your favourite molecules...</p> | ||
| − | *[http:// | + | *[http://www.gunda.hu/mol2mol/index.html Mol2Mol] |
:<p>The Mol2Mol 5.2 molecule file conversion and manipulation utility program can recognise and input/output about 40 different types of molfiles. Several utilities are also included. Has POV-Ray support.</p> | :<p>The Mol2Mol 5.2 molecule file conversion and manipulation utility program can recognise and input/output about 40 different types of molfiles. Several utilities are also included. Has POV-Ray support.</p> | ||
| − | *[http:// | + | *[http://www.tucows.com/preview/9805 MOLMOL] |
| − | :<p>MOLecule analysis and MOLecule display</p> | + | :<p>MOLecule analysis and MOLecule display |
| + | [http://web.archive.org/web/20080531045616/http://hugin.ethz.ch/wuthrich/software/molmol/ Archive to the original page] | ||
| + | </p> | ||
*[http://www.chem.ufl.edu/~der/der_pov2.htm Molpov] | *[http://www.chem.ufl.edu/~der/der_pov2.htm Molpov] | ||
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:<p>ORTEP-3 for Windows is chemical structure drawing tool by Louis J. Farrugia with POV-Ray and Raster3D support. Reads SHELX, CIF, Sybyl MOL, XYZ, PDB and other file formats.</p> | :<p>ORTEP-3 for Windows is chemical structure drawing tool by Louis J. Farrugia with POV-Ray and Raster3D support. Reads SHELX, CIF, Sybyl MOL, XYZ, PDB and other file formats.</p> | ||
| − | *[http://www.suchanek.org/egsweb_org/pdb2povf/pdb2pov.html pdb2pov] | + | *[http://web.archive.org/web/20080215194048/http://www.suchanek.org/egsweb_org/pdb2povf/pdb2pov.html pdb2pov] |
:<p>pdb2pov: a command line pdb file to pov-ray converter by Eric G. Suchanek.</p> | :<p>pdb2pov: a command line pdb file to pov-ray converter by Eric G. Suchanek.</p> | ||
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*[http://xray.bmc.uu.se/markh/notes/howto/molray.html The Molray molecular graphics web interface] | *[http://xray.bmc.uu.se/markh/notes/howto/molray.html The Molray molecular graphics web interface] | ||
:<p>Molray is a web interface to POV-Ray for producing high-quality molecular - graphics images from O plot files and other sources.</p> | :<p>Molray is a web interface to POV-Ray for producing high-quality molecular - graphics images from O plot files and other sources.</p> | ||
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<p class="QTNavBar">End of Category: [[KB:Programs|Go Back to the Categories List]]</p> | <p class="QTNavBar">End of Category: [[KB:Programs|Go Back to the Categories List]]</p> | ||
[[Category:POV-Ray Links Collection]] | [[Category:POV-Ray Links Collection]] | ||
Latest revision as of 20:10, 3 July 2010
A listing of chemical / molecular modelling sites in alphabetical order.
Biodesigner is a molecular modeling and visualization program for personal computers. The program is freely available for downloading. Biodesigner is capable of creating homologous models of proteins, evaluate, and refine the models. Bundled with protein sequence editor. Supports POV format output.
FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information. FTDock implements the Fourier correlation algorithm of Katchalski-Katzir and coworkers plus an electrostatics function amenable to Fourier correlation that was developed in this laboratory.
Chime allows you to view PDB (protein data base ) files from within your browser. Versions available for both the Windows and Mac platforms. Need to login to download
DINO uses OpenGL for realtime visualization of biological structures, surfaces, scalar fields and topographs. POV-Ray output is supported
A web based Dynamical systems laboratory where the scenes were built with Povray.
Garlic, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, linux, free software download, open source software.
Convert Mol/BobScript output to POV-Ray and Raster3D format. Gl_render is a front-end to MolScript / BobScript, POV-Ray and Raster3D.
JOELib is a platform independent open source computational chemistry package written in Java with output support for POV-Ray..
The MacroModel program suite from Schr÷dinger, Inc. allows the graphical construction of complex chemical structures and the application of molecular mechanics and dynamics techniques in vacuo or in solution.
mm2pov is a program which converts a MacroModel data file into a Persistence of Vision blob object. This allows you to ray-trace some really pretty pictures of your favourite molecules...
The Mol2Mol 5.2 molecule file conversion and manipulation utility program can recognise and input/output about 40 different types of molfiles. Several utilities are also included. Has POV-Ray support.
MOLecule analysis and MOLecule display
MolPOV is a graphics file converter that reads Brookhaven Protein Data Bank format files and produces a ready-to-render input file for the Persistence of Vision ray tracer (POV-Ray). The PDB files can be from the Brookhaven PDB itself or from any molecular modeling program that can store structures in the PDB format
ORTEP-3 for Windows is chemical structure drawing tool by Louis J. Farrugia with POV-Ray and Raster3D support. Reads SHELX, CIF, Sybyl MOL, XYZ, PDB and other file formats.
pdb2pov: a command line pdb file to pov-ray converter by Eric G. Suchanek.
PovChem is a chemical visualization and illustration program with a new graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration - colors, atom and bond radii, view orientation, etc. It will even calculate and display hydrogen bonds. It then exports the picture in POV-Ray format, which allows you to render the image with a state-of-the-art raytracer, giving high-quality images at any resolution, for anything from web page thumbnails to full-size high-resolution images for journal covers, advertisements, posters, anything! By Paul A. Thiessen
Free molecular ray-casting software. Runs under Linux, Unix, Mac and Windows. PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation.
Editor for chemical structures (automatic generation of 3D coords) and Interfaces to several programs (e.g. qc-Programs, POV-Ray) by Jörg Dettmann.
DeepView - Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. . Has POV-Ray support
Molray is a web interface to POV-Ray for producing high-quality molecular - graphics images from O plot files and other sources.
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