Bioinformatics: Difference between revisions

Revision as of 19:25, 4 September 2010

http://pdomains.sdsc.edu offering an interface for comparing a number of different methods for automatic domain definition. For domain interfaces 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.
In the sequence tab for each PDB entry, (for example, http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1AJH), the domain assignment from SCOP, DP, CATH etc. are given.

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

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

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

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 * 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.
+* In the sequence tab for each PDB entry, (for example, http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1AJH), the domain assignment from SCOP, DP, CATH etc. are given.
 === Functional annotation ===