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
- pKa of protein - evaluated in: Crystallography Reviews, Volume 15, Issue 4 October 2009 , pages 231 - 259 An evaluation review of the prediction of protonation states in proteins versus crystallographic experiment Authors: Stuart J. Fisher; James Wilkinson; Richard H. Henchman; John R. Helliwell available at:- http://www.informaworld.com/smpp/content~db=all~content=a915050320~tab=content~order=page
- Programs for visualization (see also Model building)
- Links to Bioinformatics websites
- programs with chemistry knowledge, e.g. to build 3D-coordinates from 2D drawings
- modeling of glycosylation with GlyProt
- PDBeStatistics and some explanation of it