The classification of protein structures based on the sequential and structural similarity, and the database of representative protein chains (PDB-REPRDB)

NOGUCHI TAMOTSU, AKIYAMA YUTAKA, ONIZUKA KENTARO, ANDO MAKOTO

Bibliographic Information

Other Title

タンパク質立体構造の配列および原子間距離による分類と非冗長化されたPDB代表タンパク質チェインデータベース(PDB-REPRDB)の作成

Description

The Protein Data Bank (PDB) is a rich library of atomic-coordinata data of biological macromolecules. The PDB entries has been increasing rapidly by the improvement of X-ray crystallography and NMR experimental techniques, and the number of current entries is more than 7,500 (3.4Gbytes), though not all entries are competent for the purpose of computational protein structure analysis. A lot of entries have insufficiently-refined coordinate data, or have some or many similar entries in terms of structural or sequential similarity. Thus the need for a classification procedure of protein sturcures has become quit obvious. We have proposed a representative chain database PDB-REPRDB, which startegy of selection is based on the sequential and structural similarity. In this paper, we have developed a representative chain database PDB-REPRDB, and we report the MPI-parallelization of our automatic construction system for PDB-REPRDB. Now that a calculation of a representative set can be done within 1.5 hours rather than 1 week, with 110-folds speed-up achieved in this study. We have opened a WWW service for the PDB-REPRDB, which have been accessed more than 2100 times.

Journal

IPSJ SIG Notes

IPSJ SIG Notes 21 31-36, 1998-10-07

Information Processing Society of Japan (IPSJ)

Details 詳細情報について

CRID: 1571980077129537792

NII Article ID: 110002936322

NII Book ID: AN10505667

ISSN: 09196072

Text Lang: ja

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