TY - CHAP
T1 - Protein-protein interfaces
T2 - Recognition of similar spatial and chemical organizations
AU - Shulman-Peleg, Alexandra
AU - Mintz, Shira
AU - Nussinov, Ruth
AU - Wolfson, Haim J.
PY - 2004
Y1 - 2004
N2 - Protein-protein interfaces, which are regions of interaction between two protein molecules, contain information about patterns of interacting functional groups. Recognition of such patterns is useful both for prediction of binding partners and for the development of drugs that can interfere with the formation of the protein-protein complex. We present a novel method, Interface-to- interface (I2I)-SiteEngine, for structural alignment between two protein-protein interfaces. The method simultaneously aligns two pairs of binding sites that constitute an interface. The method is based on recognition of similarity of physico-chemical properties and shapes. It assumes no similarity of sequences or folds of the proteins that comprise the interfaces. Similarities between interfaces recognized by I2I-SiteEngine provide an insight into the interactions that are essential for the formation of the complex and can be related to its function. Its high efficiency makes it suitable for large scale database searches and classifications.
AB - Protein-protein interfaces, which are regions of interaction between two protein molecules, contain information about patterns of interacting functional groups. Recognition of such patterns is useful both for prediction of binding partners and for the development of drugs that can interfere with the formation of the protein-protein complex. We present a novel method, Interface-to- interface (I2I)-SiteEngine, for structural alignment between two protein-protein interfaces. The method simultaneously aligns two pairs of binding sites that constitute an interface. The method is based on recognition of similarity of physico-chemical properties and shapes. It assumes no similarity of sequences or folds of the proteins that comprise the interfaces. Similarities between interfaces recognized by I2I-SiteEngine provide an insight into the interactions that are essential for the formation of the complex and can be related to its function. Its high efficiency makes it suitable for large scale database searches and classifications.
UR - http://www.scopus.com/inward/record.url?scp=35048856940&partnerID=8YFLogxK
U2 - 10.1007/978-3-540-30219-3_17
DO - 10.1007/978-3-540-30219-3_17
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AN - SCOPUS:35048856940
SN - 3540230181
SN - 9783540230182
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 194
EP - 205
BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
A2 - Jonassen, Inge
A2 - Kim, Junhyong
PB - Springer Verlag
ER -