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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 |
2004-1-23
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pubmed:abstractText |
Hydrogen bond, hydrophobic and vdW interactions are the three major non-covalent interactions at protein-protein interfaces. We have developed a method that uses only these properties to describe interactions between proteins, which can qualitatively estimate the individual contribution of each interfacial residue to the binding and gives the results in a graphic display way. This method has been applied to analyze alanine mutation data at protein-protein interfaces. A dataset containing 13 protein-protein complexes with 250 alanine mutations of interfacial residues has been tested. For the 75 hot-spot residues (deltadelta G > or = 1.5 kcal mol(-1)), 66 can be predicted correctly with a success rate of 88%. In order to test the tolerance of this method to conformational changes upon binding, we utilize a set of 26 complexes with one or both of their components available in the unbound form. The difference of key residues exported by the program is 11% between the results using complexed proteins and those from unbound ones. As this method gives the characteristics of the binding partner for a particular protein, in-depth studies on protein-protein recognition can be carried out. Furthermore, this method can be used to compare the difference between protein-protein interactions and look for correlated mutation.
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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 |
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pubmed:status |
MEDLINE
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pubmed:month |
Feb
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pubmed:issn |
0948-5023
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:volume |
10
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
44-54
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pubmed:dateRevised |
2009-11-19
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pubmed:meshHeading |
pubmed-meshheading:14634848-Alanine,
pubmed-meshheading:14634848-Animals,
pubmed-meshheading:14634848-Aspartic Acid Endopeptidases,
pubmed-meshheading:14634848-Binding Sites,
pubmed-meshheading:14634848-Chickens,
pubmed-meshheading:14634848-Computational Biology,
pubmed-meshheading:14634848-Databases, Protein,
pubmed-meshheading:14634848-HIV Protease,
pubmed-meshheading:14634848-Hydrogen Bonding,
pubmed-meshheading:14634848-Ligands,
pubmed-meshheading:14634848-Models, Molecular,
pubmed-meshheading:14634848-Molecular Conformation,
pubmed-meshheading:14634848-Muramidase,
pubmed-meshheading:14634848-Mutation,
pubmed-meshheading:14634848-Protein Binding,
pubmed-meshheading:14634848-Protein Conformation,
pubmed-meshheading:14634848-Protein Folding,
pubmed-meshheading:14634848-Protein Interaction Mapping,
pubmed-meshheading:14634848-Proteins,
pubmed-meshheading:14634848-Structural Homology, Protein,
pubmed-meshheading:14634848-Structure-Activity Relationship,
pubmed-meshheading:14634848-Thermodynamics
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pubmed:year |
2004
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pubmed:articleTitle |
Structure-based method for analyzing protein-protein interfaces.
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pubmed:affiliation |
State Key Laboratory of Structural Chemistry for Stable and Unstable Species, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China.
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pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't
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