Bioinformatics: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
m (→Structure only) |
||
| Line 21: | Line 21: | ||
* [http://www.ebi.ac.uk/thornton-srv/databases/procognate/ database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam] | * [http://www.ebi.ac.uk/thornton-srv/databases/procognate/ database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam] | ||
* [http://robetta.bakerlab.org/alascansubmit.jsp Rosetta Alanine Scanning] each residue in a interface is mutated to Ala; local minimisation is performed, and the binding energy is calculated | * [http://robetta.bakerlab.org/alascansubmit.jsp Rosetta Alanine Scanning] each residue in a interface is mutated to Ala; local minimisation is performed, and the binding energy is calculated | ||
* [http://pdomains.sdsc.edu] offering an interface for comparing a number of different methods for ''automatic domain definition'' | |||
=== Functional annotation === | === Functional annotation === | ||
Revision as of 08:35, 19 October 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
- [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
Other stuff
- Programs for visualization (see also Model building)