Bioinformatics: Difference between revisions
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(→Structure only: add procognate server) |
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* [[Morphing]] | * [[Morphing]] | ||
* [[Programs for representing the surface of a channel inside protein]] | * [[Programs for representing the surface of a channel inside protein]] | ||
* [http://www.ebi.ac.uk/thornton-srv/databases/procognate/ database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam] | |||
=== Docking === | === Docking === | ||
Revision as of 11:58, 2 December 2008
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
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)