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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
1
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pubmed:dateCreated |
2003-6-4
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pubmed:abstractText |
We present a very efficient rigid "unbound" soft docking methodology, which is based on detection of geometric shape complementarity, allowing liberal steric clash at the interface. The method is based on local shape feature matching, avoiding the exhaustive search of the 6D transformation space. Our experiments at CAPRI rounds 1 and 2 show that although the method does not perform an exhaustive search of the 6D transformation space, the "correct" solution is never lost. However, such a solution might rank low for large proteins, because there are alternatives with significantly larger geometrically compatible interfaces. In many cases this problem can be resolved by successful a priori focusing on the vicinity of potential binding sites as well as the extension of the technique to flexible (hinge-bent) docking. This is demonstrated in the experiments performed as a lesson from our CAPRI experience.
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pubmed:grant |
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
http://linkedlifedata.com/resource/pubmed/chemical/Antibodies,
http://linkedlifedata.com/resource/pubmed/chemical/Antigens, Viral,
http://linkedlifedata.com/resource/pubmed/chemical/Bacterial Proteins,
http://linkedlifedata.com/resource/pubmed/chemical/Capsid Proteins,
http://linkedlifedata.com/resource/pubmed/chemical/Exotoxins,
http://linkedlifedata.com/resource/pubmed/chemical/HPr kinase,
http://linkedlifedata.com/resource/pubmed/chemical/Hemagglutinin Glycoproteins...,
http://linkedlifedata.com/resource/pubmed/chemical/Macromolecular Substances,
http://linkedlifedata.com/resource/pubmed/chemical/Membrane Proteins,
http://linkedlifedata.com/resource/pubmed/chemical/Phosphoenolpyruvate Sugar...,
http://linkedlifedata.com/resource/pubmed/chemical/Protein-Serine-Threonine Kinases,
http://linkedlifedata.com/resource/pubmed/chemical/Proteins,
http://linkedlifedata.com/resource/pubmed/chemical/Receptors, Antigen, T-Cell...,
http://linkedlifedata.com/resource/pubmed/chemical/SpeA protein, Streptococcus pyogenes,
http://linkedlifedata.com/resource/pubmed/chemical/VP6 protein, Rotavirus,
http://linkedlifedata.com/resource/pubmed/chemical/alpha-Amylases,
http://linkedlifedata.com/resource/pubmed/chemical/phosphocarrier protein HPr
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pubmed:status |
MEDLINE
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pubmed:month |
Jul
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pubmed:issn |
1097-0134
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pubmed:author |
pubmed-author:BarzilaiAdiA,
pubmed-author:BenyaminiHadarH,
pubmed-author:DrorOranitO,
pubmed-author:HalperinInbalI,
pubmed-author:HaspelNuritN,
pubmed-author:InbarYuvalY,
pubmed-author:NussinovRuthR,
pubmed-author:PolakVladimirV,
pubmed-author:Schneidman-DuhovnyDinaD,
pubmed-author:ShatskyMaximM,
pubmed-author:WolfsonHaim JHJ
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pubmed:issnType |
Electronic
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pubmed:day |
1
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pubmed:volume |
52
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
107-12
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pubmed:dateRevised |
2008-11-21
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pubmed:meshHeading |
pubmed-meshheading:12784375-Algorithms,
pubmed-meshheading:12784375-Antibodies,
pubmed-meshheading:12784375-Antigens, Viral,
pubmed-meshheading:12784375-Bacterial Proteins,
pubmed-meshheading:12784375-Binding Sites,
pubmed-meshheading:12784375-Capsid Proteins,
pubmed-meshheading:12784375-Exotoxins,
pubmed-meshheading:12784375-Hemagglutinin Glycoproteins, Influenza Virus,
pubmed-meshheading:12784375-Macromolecular Substances,
pubmed-meshheading:12784375-Membrane Proteins,
pubmed-meshheading:12784375-Models, Molecular,
pubmed-meshheading:12784375-Phosphoenolpyruvate Sugar Phosphotransferase System,
pubmed-meshheading:12784375-Protein Interaction Mapping,
pubmed-meshheading:12784375-Protein-Serine-Threonine Kinases,
pubmed-meshheading:12784375-Proteins,
pubmed-meshheading:12784375-Receptors, Antigen, T-Cell, alpha-beta,
pubmed-meshheading:12784375-alpha-Amylases
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pubmed:year |
2003
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pubmed:articleTitle |
Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking.
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pubmed:affiliation |
School of Computer Science, Beverly and Raymond Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
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pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, P.H.S.,
Research Support, Non-U.S. Gov't,
Evaluation Studies
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