Useful links

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		Molecular visualization 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

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		Secondary Structure Element alignment
TOP			Secondary Structure Element alignment
VAST	http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html	NA	Vector alignment

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