Bioinformatics
Sequence only
Sequence to structure
Structure to Sequence
Structure only
- Servers for ligand topologies/parameters
- Servers and programs for protein structure analysis
- Programs for nucleic acid structure analysis
- Morphing
- Programs for representing the surface of a channel inside protein
- database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam
- Rosetta Alanine Scanning each residue in a interface is mutated to Ala; local minimisation is performed, and the binding energy is calculated
- GOdot webserver for predicting function from structure (see http://dx.plos.org/10.1371%2Fjournal.pcbi.1000105)
Docking
- ClusPro - easy to use web interface
- Rosetta can do much more than just docking, but is difficult to use
- 3D-dock - uses an algorithm that mainly looks at surface complimentarity between the two proteins
- Dave Ritchie's Hex program - it is blisteringly quick
- Haddock - recommended by Tassos
- AutoDock - Wiki at https://www.nbcr.net/pub/wiki/index.php?title=AutoDock
Other stuff
- Programs for visualization (see also Model building)