Crystallography Research Today is a free monthly online journal that collates and summarizes the latest research about Crystallography, including details on x-ray crystals, techniques, analyses, structures.

PreBI: prediction of biological interfaces of proteins in crystals.

Tsuchiya Y, Kinoshita K, Ito N, Nakamura H

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

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/.

Published 17 July 2006 in Nucleic Acids Res, 34: W320-4.
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