Bioinformatics: Difference between revisions
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* [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 | ||
== Functional annotation == | |||
* [http://godot.bioinf.mpi-inf.mpg.de GOdot] webserver for predicting function from structure (see http://dx.plos.org/10.1371%2Fjournal.pcbi.1000105) | * [http://godot.bioinf.mpi-inf.mpg.de GOdot] webserver for predicting function from structure (see http://dx.plos.org/10.1371%2Fjournal.pcbi.1000105) | ||
* [http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/ ProFunc] Analysis of a protein's 3D structure to help identify its likely biochemical function | |||
* [http://kb.psi-structuralgenomics.org/KB/index1.jsp?pageshow=39 Annotation] PSI Stuctural Genomics knowledgebase | |||
=== Docking === | === Docking === | ||
Revision as of 11:59, 16 September 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
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)