Bioinformatics
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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
- [1] offering an interface for comparing a number of different methods for automatic domain definition
Functional annotation
- GOdot webserver for predicting function from structure (see http://dx.plos.org/10.1371%2Fjournal.pcbi.1000105)
- ProFunc Analysis of a protein's 3D structure to help identify its likely biochemical function
- Annotation PSI Stuctural Genomics knowledgebase
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
- DockBlaster - runs DOCK 3.5.54; there's a wiki
Other stuff
- Programs for visualization (see also Model building)
- programs with chemistry knowledge, e.g. to build 3D-coordinates from 2D drawings