Comparison-based approaches to the automated prediction of
interesting 3D sites in a protein structure
A side-by-side comparison of available
techniques and tools
[October 27, 2005]
This page was transferred to
wikiomics.org, the bioinformatics wiki
and is evolving there.
The quality of this document depends on your feedback. Please notify me of any erroneous or missing information (email: Martin Jambon <martin@mjambon.com>).
For now, only methods which can be used directly on the web are listed, sorry.
Also, this document is exclusively restricted to the different ways of finding similarities between a given protein structure and some existing or averaged 3D sites. It excludes methods which are based only on the amino acid sequence (such as Prosite search) or which do not return correspondences between 3D sites.
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| Name (alphabetic order) | Basic elements in the representation of a protein | Molecular shape is used | Sites can match partially | Rigid superposition of sites | Web server | Scan protein vs. functional sites online | Scan site vs. proteins online | Protein vs. protein comparison online | Conditions of use | Major references | Notes |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PdbFun | centroid of amino acids | no | yes | yes | http://pdbfun.uniroma2.it/ | yes | yes | yes | free access | features and user interface (no details concerning the comparison algorithm in this paper) | |
| PDBSiteScan | amino acids represented by the C, C-alpha and N atoms of the main chain | no | yes | yes, using MDM (maximum distance mismatch) | http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsitescan/ | yes | no | no | free access | PDBSiteScan, PDBSite | |
| PINTS | selected atoms from lateral chains | no | yes | yes (using RMSD) | http://www.russell.embl.de/pints/ | yes | yes | yes | web version freely accessible to everyone | method, assessment | |
| PROCAT/TESS/Jess/Catalytic Site Atlas | atoms | no | no | yes (using RMSD) | http://www.ebi.ac.uk/thornton-srv/databases/CSA/ | yes (catalytic sites) | no | no | free access | original algorithm, faster algorithm (TESS), Jess algorithm, successor of TESS, CSA, CSA, CSA | Catalytic Site Atlas (CSA) is the successor of the PROCAT webserver and database of templates of catalytic sites |
| pvSOAR | centroids of amino acids forming pockets and the pseudosequence they form (sequence without non-pocket residues) | yes | yes | yes | http://pvsoar.bioengr.uic.edu/ | yes (pockets) | pocket vs. database of pockets | no | free access | method and validation, web server | |
| SiteEngine | surface exposed functional groups that describe the physico-chemical properties of amino acids | yes | yes | yes (using RMSD) | http://bioinfo3d.cs.tau.ac.il/SiteEngine/ | no | no | yes (protein vs. site) | web server open to anyone, downloadable software under the terms of a specific license | method | |
| SPASM/RIGOR | C-alpha or centroid of lateral chains | no | yes | yes (using RMSD) | http://portray.bmc.uu.se/cgi-bin/spasm/scripts/spasm.pl | yes (RIGOR) | yes (SPASM) | no | free access | method (SPASM and RIGOR), (reprint) | |
| SuMo | selected triplets of functional groups of heterogeneous geometric types, with local molecular shape around each triplet given by surrounding non-H atoms | yes | yes | no | http://sumo-pbil.ibcp.fr/ | yes | yes | yes (expert mode only) | web version freely accessible to non-profit users, custom installation and services available on demand from MEDIT | method (about 60% obsolete), detailed method (95% up-to-date), patent WO03104388 |