Molecular modeling and visualization software: Difference between revisions
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*[http://hollow.sourceforge.net/ HOLLOW] is not a stand-alone molecular visualization program; however, it facilitates the production of surface images of proteins. You input a PDB file and get out a PDB file of dummy water atoms that forms a "cast" of the voids and channels of a protein. | *[http://hollow.sourceforge.net/ HOLLOW] is not a stand-alone molecular visualization program; however, it facilitates the production of surface images of proteins. You input a PDB file and get out a PDB file of dummy water atoms that forms a "cast" of the voids and channels of a protein. | ||
* [http://rinalyzer.de/ RINalyzer] enables analyzing and visualizing residue interaction networks (RINs) constructed from the three-dimensional structure of a protein as stored in PDB files from the Protein Data Bank. RINalyzer allows simultaneous, interactive 2D visualization and exploration of a RIN in [http://www.cytoscape.org/ Cytoscape], in conjunction with the molecular 3D structure visualized in the [http://www.cgl.ucsf.edu/chimera/ UCSF Chimera] visulization/modelling system. [http://www.cytoscape.org/ Cytoscape] is a free, open-source software platform for the analysis and visualization of molecular interaction networks. RIN Data for any PDB entry can be downloaded [http://rinalyzer.de/rindata.php here] using the [[PDB code]], alternatively the [http://protein.cribi.unipd.it/ring/ RING web server] can be used to generate RINs. | * [http://rinalyzer.de/ RINalyzer] enables analyzing and visualizing residue interaction networks (RINs) constructed from the three-dimensional structure of a protein as stored in PDB files from the Protein Data Bank. RINalyzer allows simultaneous, interactive 2D visualization and exploration of a RIN in [http://www.cytoscape.org/ Cytoscape], in conjunction with the molecular 3D structure visualized in the [http://www.cgl.ucsf.edu/chimera/ UCSF Chimera] visulization/modelling system. [http://www.cytoscape.org/ Cytoscape] is a free, open-source software platform for the analysis and visualization of molecular interaction networks. RIN Data for any PDB entry can be downloaded [http://rinalyzer.de/rindata.php here] using the [[PDB code]], alternatively the [http://protein.cribi.unipd.it/ring/ RING web server] can be used to generate RINs. | ||
* [http://qutemol.sourceforge.net/ Qutemol] is an open source (GPL), interactive, high quality molecular visualization system. QuteMol produces images in real time by running algorithms that rely on modern graphic card features, including programmable fragment & vertex shaders, and frame and vertex buffer objects. | |||
==Free molecular modeling software== | ==Free molecular modeling software== | ||
