http://www.cs.ucdavis.edu/~koehl/



Useful links for Computational Biology



Visualization || Structure Comparison || Rotamer libraries || Homology Modelling

Visualisation


Program name Location Description
Grasp http://trantor.bioc.columbia.edu/grasp/ Visualisation package with emphasis on surface and electrostatics
Mage http://kinemage.biochem.duke.edu/kinemage/kinemage.php Generates scientific illustration presented as an interactive computer display
Molscript http://www.avatar.se/molscript/ Generates scientific illustration
MolMol http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ Molecular visualization package with emphasis on NMR data
O http://www.imsb.au.dk/~mok/o/ Molecular visualisation package with emphasis on X-ray data
Pymol http://pymol.sourceforge.net/ Open Source molecular modeling software
Rasmol http://www.umass.edu/microbio/rasmol/ Molecular visualization freeware

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Protein structure comparison


Program name Server Interface Program download Method
CE http://cl.sdsc.edu ftp://ftp.sdsc.edu/pub/sdsc/biology/CE/src/ Extension of the optimal path
DALI http://www2.ebi.ac.uk/dali http://jura.ebi.ac.uk:8765/~holm/DaliLite Distance matrix alignment
K2 http://sullivan.bu.edu/kenobi http://sullivan.bu.edu/kenobi genetic algorithm
PRISM NA http://www.columbia.edu/~ay1 Secondary Structure Element alignment
TOP http://bioinfo1.mbfys.lu.se/TOP ftp://bioinfo1.mbfys.lu.se/pub/guoguang Secondary Structure Element alignment
VAST http://www.ncbi.nlm.nih.gov/
Structure/VAST/vastsearch.html		 NA Vector alignment

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Side-chain Rotamer libraries

Library name Location
Ponder and Richards http://www.fccc.edu/research/labs/dunbrack/sidechain/ponder_richards.rot
Dunbrack and Cohen http://www.fccc.edu/research/labs/dunbrack/sidechain.html
Tuffery et al http://condor.urbb.jussieu.fr/Rotamer.php/
DeMaeyer et al http://www.fccc.edu/research/labs/dunbrack/sidechain/demaeyer.rot
Lovell et al http://kinemage.biochem.duke.edu/databases/rotamer.php

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Homology modelling packages

Name Web site
MODELLER http://guitar.rockerfeller.edu/modeller/
3D-Jigsaw http://www.bmm.icnet.uk/servers/3djigsaw/
SDSC1 http://cl.sdsc.edu/hm.html
SCWRL http://www.fccc.edu/research/labs/dunbrack/scwrl/
SWISS-MODEL http://www.expasy.ch/swissmod/SWISS-MODEL.html

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  Page last modified 22 December 2004 http://www.cs.ucdavis.edu/~koehl/BioEbook/