KiBank http://kibank.iis.u-tokyo.ac.jp/index.jsp
KiBank for in silico drug design. This database contains binding
affinity, structures of chemicals and target proteins, and many useful
links and information.
Binding Databse http://www.bindingdb.org/bind/index.jsp
The BindingDB is a public, web-accessible database of measured binding
affinities for biomolecules, genetically or chemically modified
biomolecules, and synthetic compounds.
Indonesia http://xray.bmc.uu.se/dennis/ Program from the
Biomedical Centre in Uppsala for structure-based sequence alignments.
Java-based program which can read pdf-file for superimposing the
structures and creating a sequence alignment in various file-formats.
For starting the program: prepare indonesia / indonesia
http://www.ccdc.cam.ac.uk/products/life_sciences/gold/
GOLD is a program for calculating the docking modes of small molecules
into protein binding sites. insightII
Insight II can add hydrogens to ligands at different pH-values.
Vida http://www.eyesopen.com/products/applications/vida.html
/home/gabdourf/progs/VIDANC6
source env.com
Doesn't add hydrogens to a pdb file in the right way without any
further information (atomtypes, bonds, hybrydisation,...) WatCH http://www.bch.msu.edu/labs/kuhn/web/software/WatCH/doc.html
A tool for identifying conserved water sites and analyzing their degree
of conservation using heirarchical cluster analysis of superimposed
related Protein Data Bank structures.