1,330
edits
Bioinformatics: Difference between revisions
Jump to navigation
Jump to search
→Structure only: domains
(→Other stuff: propka) |
(→Structure only: domains) |
||
| 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 | ||
* | |||
=== Domain definition === | |||
* http://pdomains.sdsc.edu offering an interface for comparing a number of different methods for ''automatic domain definition''. For domain interfaces [http://141.30.193.6/scoppi/ SCOPPI] may be helpful. | |||
* http://www.ebi.ac.uk/pdbe/docs/sifts/ a list of tab delimited files that contain all the information for each chain in the PDB. The information is also available per residue in XML format that contain additional annotation. These files are updated every week. | |||
* A collection of links to structure-based domain parsers is at http://binf.gmu.edu/ttaylor/homepagelinks.html | |||
* Domain boundaries are available through RCSB PDB RESTful web services described at: http://www.pdb.org/pdb/software/rest.do. For example, the URL http://www.pdb.org/pdb/rest/das/pdbchainfeatures/features?segment=1AJH.A returns an XML file with SCOP, CATH, DP, PDP, PFAM, InterPro domain boundaries, plus secondary structure information by DSSP, STRIDE, and the structure author. | |||
=== Functional annotation === | === Functional annotation === | ||