PreBI: prediction of biological interfaces of proteins in crystals | Zendy

Yuko Tsuchiya | Zendy; Kazutomo Kinoshita | Zendy; Nao Ito | Zendy; H. Nakamura | Zendy

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PreBI: prediction of biological interfaces of proteins in crystals

Author(s) -

Yuko Tsuchiya,

Kazutomo Kinoshita,

Nao Ito,

H. Nakamura

Publication year - 2006

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkl267

Subject(s) - protein data bank (rcsb pdb) , complementarity (molecular biology) , interface (matter) , biology , graphical user interface , computer science , crystallography , coordinate system , user interface , computational science , bioinformatics , biological system , operating system , biochemistry , artificial intelligence , chemistry , genetics , pulmonary surfactant , gibbs isotherm

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/.

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