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PreBI: prediction of biological interfaces of proteins in crystals.

ABSTRACT: PreBI is a server that predicts biological interfaces in protein crystal structures, according to the complementarity and the area of the interface. The server accepts a coordinate file in the PDB format, and all of the possible interfaces are generated automatically, according to the symmetry operations given in the coordinate file. For all of the interfaces generated, the complementarities of the electrostatic potential, hydrophobicity and shape of the interfaces are analyzed, and the most probable biological interface is identified according to the combination of the degree of complementarity derived from the database analyses and the area of the interface. The results can be checked through an interactive viewer, and the most probable complex can be downloaded as atomic coordinates in the PDB format. PreBI is available at http://pre-s.protein.osaka-u.ac.jp/~prebi/.

SUBMITTER: Tsuchiya Y

PROVIDER: S-EPMC1538861 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature

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PreBI: prediction of biological interfaces of proteins in crystals.

Tsuchiya Yuko Y Kinoshita Kengo K Ito Nobutoshi N Nakamura Haruki H

Nucleic acids research 20060701 Web Server issue

PreBI is a server that predicts biological interfaces in protein crystal structures, according to the complementarity and the area of the interface. The server accepts a coordinate file in the PDB format, and all of the possible interfaces are generated automatically, according to the symmetry operations given in the coordinate file. For all of the interfaces generated, the complementarities of the electrostatic potential, hydrophobicity and shape of the interfaces are analyzed, and the most pro ...[more]

PMID: 16844993

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