Source:http://linkedlifedata.com/resource/pubmed/id/15981266
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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
2
|
| pubmed:dateCreated |
2005-6-30
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| pubmed:abstractText |
The ICM Docking and Interface Side-Chain Optimization (ICM-DISCO) showed promising predictive results during the first CAPRI experiment by successfully finding medium- or high-accuracy models in 3 of the 7 targets. A key factor was the ability to recognize near-native rigid-body geometries in a relatively low number of alternative docking poses, together with the successful refinement of the rigid-body docking interfaces. Since then, we have focused on improving the scoring function to optimally discriminate the near-native rigid-body conformations. For that, we have defined a new desolvation descriptor for rigid-body docking, based on atomic solvation parameters (ASPs) derived from octanol-water transfer experiments. This and other new approaches have been gradually incorporated into our docking procedure during our participation on the second CAPRI experiment. Overall, we produced reasonable models for 8 of the 9 official targets. Especially encouraging were those cases in which a homology model of 1 of the subunits had to be used during the docking simulations. And not less gratifying has been the successful prediction of antibody-antigen targets in a completely automatic, unrestrained fashion. In summary, our success rate (89%) shows a consistent improvement over the previous CAPRI rounds, and suggests that a correct desolvation description is key for improved protein-protein docking predictions.
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| pubmed:language |
eng
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| pubmed:journal | |
| pubmed:citationSubset |
IM
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| pubmed:chemical | |
| pubmed:status |
MEDLINE
|
| pubmed:month |
Aug
|
| pubmed:issn |
1097-0134
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| pubmed:author | |
| pubmed:issnType |
Electronic
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| pubmed:day |
1
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| pubmed:volume |
60
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| pubmed:owner |
NLM
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| pubmed:authorsComplete |
Y
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| pubmed:pagination |
308-13
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| pubmed:dateRevised |
2008-11-21
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| pubmed:meshHeading |
pubmed-meshheading:15981266-Algorithms,
pubmed-meshheading:15981266-Animals,
pubmed-meshheading:15981266-Bacterial Proteins,
pubmed-meshheading:15981266-Binding Sites,
pubmed-meshheading:15981266-Computational Biology,
pubmed-meshheading:15981266-Computer Simulation,
pubmed-meshheading:15981266-Crystallography, X-Ray,
pubmed-meshheading:15981266-Databases, Protein,
pubmed-meshheading:15981266-Dimerization,
pubmed-meshheading:15981266-Internet,
pubmed-meshheading:15981266-Macromolecular Substances,
pubmed-meshheading:15981266-Models, Molecular,
pubmed-meshheading:15981266-Models, Statistical,
pubmed-meshheading:15981266-Molecular Conformation,
pubmed-meshheading:15981266-Protein Binding,
pubmed-meshheading:15981266-Protein Conformation,
pubmed-meshheading:15981266-Protein Folding,
pubmed-meshheading:15981266-Protein Interaction Mapping,
pubmed-meshheading:15981266-Protein Structure, Tertiary,
pubmed-meshheading:15981266-Proteomics,
pubmed-meshheading:15981266-Reproducibility of Results,
pubmed-meshheading:15981266-Sequence Alignment,
pubmed-meshheading:15981266-Software,
pubmed-meshheading:15981266-Static Electricity,
pubmed-meshheading:15981266-Structural Homology, Protein
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| pubmed:year |
2005
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| pubmed:articleTitle |
Improving CAPRI predictions: optimized desolvation for rigid-body docking.
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| pubmed:affiliation |
Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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| pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't
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