Bioinformatics: Difference between revisions
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* [[Prediction of structure from sequence: servers and programs]] | * [[Prediction of structure from sequence: servers and programs]] | ||
* [[Mapping sequence alignment to a structure]] | |||
== Structure to Sequence == | == Structure to Sequence == | ||
Revision as of 00:10, 30 January 2009
Sequence only
Sequence to structure
- Prediction of structure from sequence: servers and programs
- Mapping sequence alignment to a 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
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)