Linked Life Data

19406922

Source:http://linkedlifedata.com/resource/pubmed/id/19406922

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
Web Server issue
pubmed:dateCreated
2009-6-30
pubmed:abstractText
SplitPocket (http://pocket.uchicago.edu/) is a web server to identify functional surfaces of protein from structure coordinates. Using the Alpha Shape Theory, we previously developed an analytical approach to identify protein functional surfaces by the geometric concept of a split pocket, which is a pocket split by a binding ligand. Our geometric approach extracts site-specific spatial information from coordinates of structures. To reduce the search space, probe radii are designed according to the physicochemical textures of molecules. The method uses the weighted Delaunay triangulation and the discrete flow algorithm to obtain geometric measurements and spatial patterns for each predicted pocket. It can also measure the hydrophobicity on a surface patch. Furthermore, we quantify the evolutionary conservation of surface patches by an index derived from the entropy scores in HSSP (homology-derived secondary structure of proteins). We have used the method to examine approximately 1.16 million potential pockets and identified the split pockets in >26,000 structures in the Protein Data Bank. This integrated web server of functional surfaces provides a source of spatial patterns to serve as templates for predicting the functional surfaces of unbound structures involved in binding activities. These spatial patterns should also be useful for protein functional inference, structural evolution and drug design.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-10360179, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-12402356, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-12876308, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-12948498, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-14681403, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-15701681, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-16251508, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-16322579, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-16844972, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-18361455, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-19154742, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-2017436, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-9741840, http://linkedlifedata.com/resource/pubmed/commentcorrection/19406922-9761470
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jul
pubmed:issn
1362-4962
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
37
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
W384-9
pubmed:dateRevised
2011-8-24
pubmed:meshHeading
pubmed:year
2009
pubmed:articleTitle
SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns.
pubmed:affiliation
Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural