Nucleic Acids Research, 2001, Vol. 29, No. 1 219-220
© 2001 Oxford University Press
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)
1Computational Biology Research Laboratory, Electrotechnical Laboratory, 1-1-4 Umezono, Tsukuba, Ibaraki 305-5868, Japan and 2Department of Informatics and Mathematical Science, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). The previous version of PDB-REPRDB provided 48 representative sets, whose similarity criteria were predetermined, on the WWW. The current version is designed so that the user may obtain a quick selection of representative chains from PDB. The selection of representative chains can be dynamically configured according to the user’s requirement. The WWW interface provides a large degree of freedom in setting parameters, such as cut-off scores of sequence and structural similarity. One can obtain a representative list and classification data of protein chains from the system. The current database includes 20 457 protein chains from PDB entries (August 6, 2000). The system for PDB-REPRDB is available at the Parallel Protein Information Analysis system (PAPIA) WWW server (http://www.rwcp.or.jp/papia/).
* To whom correspondence should be addressed. Tel: +81 298 61 5080; Fax: +81 298 61 5722; Email: tnoguchi@etl.go.jp
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