Linked Life Data

19569185

Source:http://linkedlifedata.com/resource/pubmed/id/19569185

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2010-2-3
pubmed:abstractText
Solvent dipole ordering (SDO), introduced by Higo et al. (Proteins Struct Funct Genet 2000, 40, 193), is an entity that captures an aspect of hydration structure. We have studied SDO in the ligand binding site of two proteins (FK506 binding protein and dihydrofolate reductase) and found that the high SDO regions overlap significantly with the 3D structures of known inhibitors bound to the proteins. Thus, the SDO region might be used to predict the preferred molecular shape of ligands that bind to a protein. Based on this finding, we propose a novel docking procedure using model molecules that mimic the shape of the SDO region. To prove the validity of thisapproach, we performed a redocking experiment for p38 mitogen-activated protein kinase ligands using model molecules for search queries; we succeeded in identifying the binding conformations and binding modes of known inhibitors.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Mar
pubmed:issn
1096-987X
pubmed:author
pubmed:copyrightInfo
(c) 2009 Wiley Periodicals, Inc.
pubmed:issnType
Electronic
pubmed:volume
31
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
791-6
pubmed:meshHeading
pubmed:year
2010
pubmed:articleTitle
Ligand shape emerges in solvent dipole ordering region at ligand binding site of protein.
pubmed:affiliation
Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501 Japan. murata@pharm.kyoto-u.ac.jp
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't