Wikiomics:Searching for 3D functional sites in a protein structure
Given a protein structure, which are the potentially interesting sites? Approaches which are based only on sequence patterns or backbone architecture are often insufficient to find similarities between sites of similar biochemical function.
The set of methods which are shown here use the 3D arrangement of the atoms of proteins to find putative functional sites, such as ligand binding sites or catalytic sites.
Search by comparison against annotated sites
Comparing 3D structures locally at the atomic level is not a simple problem, and there is no standard method in this field. However, many of these recent techniques are available from web servers, which makes them relatively easy to use.
An advantage of comparing a query protein structure against 3D sites of known biological activity is that both sites can be compared and the similarity can be further investigated either visually or using other tools.
Methods and tools
PdbFun  is a web server for the identification of local structural similarities between annotated residues in proteins, gives fast access to the whole PDB organized as a database of annotated residues, helps selecting any residue subset by combining the available features, compares query and target selections with a fast and sequence-independent 3D comparison algorithm representing each amino acid by one point located at its centroid.
PINTS [4, 5] defines types of atoms for certain atoms of the lateral chains of amino acids. 2 atoms of the same type such as an oxygen of a carboxyl group (in Asp or Glu) can be considered as equivalent. The search is based on interatomic distances and the scoring is based on Wikiomics:RMSD values.
pvSOAR [12, 13] uses centroids of amino acids forming pockets and the pseudosequence they form: if a pocket is made of amino acids Ala45, Tyr12, Ser124 and His32 then the corresponding sequence would be Tyr-Ala-His-Ser. The default comparison procedure uses an alignment between the sequences associated with 2 pockets. This constraint can be removed if only 2 pockets are being compared.
SiteEngine  uses surface exposed functional groups that describe the physico-chemical properties of amino acids. It is possible to compare a protein structure against a given site on the web server. The program is also available for download.
SPASM/RIGOR  was the first webserver to propose sequence- and fold-independent search in 3D structures of proteins. It represents each residue by it's C-alpha or the centroid of the lateral chain.
SuMo [16, 17, 18] uses chemical groups with their own geometry and symmetry plus a complementary local shape comparison technique. It does not require a low Wikiomics:RMSD between 2 sites to consider them as similar although local pairwise matching is required. Given a protein structure, it will scan the PDB for similar ligand binding sites and return a list of sites, sorted by decreasing size. Clicking on each individual result gives a parallel view of the matched sites.
Prediction of functional sites from geometrical or physico-chemical properties
These tools do not try to match 3D sites between a query and sites of biological importance. Based on the geometry or the chemistry of the protein sites, they are associated with a given function.
- SARIG  predicts functional sites using residue interaction graphs (contact maps)
- WebFEATURE [20, 21] scans a protein structure for local environments of a given type. An RNA version exists too, naFEATURE .
- THEMATICS [23, 24, 25] catalytic sites are predicted from deviations in theoretical titration curves of proteins
Prediction using phylogenetic information
Combined with projections onto 3D structures, the degree of conservation of aligned residues within a family of proteins can indicate amino acids which are functionally important.
- Evolutionary Trace (Cambridge) [26, 27]
- Evolutionary Trace Viewer and Evolutionary Trace report_maker (Baylor) [26, 28]
- ConSurf 
- Ausiello G, Zanzoni A, Peluso D, Via A, and Helmer-Citterich M. . pmid:15980442.
- Ivanisenko VA, Pintus SS, Grigorovich DA, and Kolchanov NA. . pmid:15215447.
- Ivanisenko VA, Pintus SS, Grigorovich DA, and Kolchanov NA. . pmid:15608173.
- Russell RB. . pmid:9642096.
- Stark A, Sunyaev S, and Russell RB. . pmid:12595245.
read pints_method first
- Wallace AC, Laskowski RA, and Thornton JM. . pmid:8762132.
- Porter CT, Bartlett GJ, and Thornton JM. . pmid:14681376.
- Bartlett GJ, Porter CT, Borkakoti N, and Thornton JM. . pmid:12421562.
- Torrance JW, Bartlett GJ, Porter CT, and Thornton JM. . pmid:15755451.
- Wallace AC, Borkakoti N, and Thornton JM. . pmid:9385633.
successor of PROCAT procat
- Barker JA and Thornton JM. . pmid:12967960.
successor of TESS tess
- Binkowski TA, Adamian L, and Liang J. . pmid:12948498.
- Binkowski TA, Freeman P, and Liang J. . pmid:15215448.
- Shulman-Peleg A, Nussinov R, and Wolfson HJ. . pmid:15147845.
- Kleywegt GJ. . pmid:9917419.
- Jambon M, Imberty A, Deléage G, and Geourjon C. . pmid:12833538.
describes the basic method, which has been considerably refined since. Read sumo_method for a good understanding of the current method and the concepts on which it relies.
- Jambon M, Andrieu O, Combet C, Deléage G, Delfaud F, and Geourjon C. . pmid:16141250.
application note about the SuMo web server
- Jambon M. A bioinformatic system for searching functional similarities in 3D structures of proteins. PhD thesis, 2003.
- Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, and Pietrokovski S. . pmid:15544817.
- Wei L and Altman RB. . pmid:9697207.
- Liang MP, Banatao DR, Klein TE, Brutlag DL, and Altman RB. . pmid:12824318.
- Banatao DR, Altman RB, and Klein TE. . pmid:12888505.
- Ko J, Murga LF, Wei Y, and Ondrechen MJ. . pmid:15961465.
- Shehadi IA, Abyzov A, Uzun A, Wei Y, Murga LF, Ilyin V, and Ondrechen MJ. . pmid:15751116.
- Ko J, Murga LF, André P, Yang H, Ondrechen MJ, Williams RJ, Agunwamba A, and Budil DE. . pmid:15739204.
- Lichtarge O, Bourne HR, and Cohen FE. . pmid:8609628.
- Innis CA, Shi J, and Blundell TL. . pmid:11239083.
- Mihalek I, Res I, and Lichtarge O. . pmid:15037084.
- Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, and Ben-Tal N. . pmid:12499312.
- Polacco BJ and Babbitt PC. . pmid:16410325.
uses the same technique as SPASM spasm_rigor
- Schmitt S, Kuhn D, and Klebe G. . pmid:12381328.
one of the most advanced technique with SuMo sumo2003 sumo2005 sumo_method, but not available online (?). (more details needed)