PDB-REPRDB: A Database of Representative
Protein Chains in PDB (Protein Data Bank)

Tamotsu NOGUCHI, Kentaro ONIZUKA, Yutaka AKIYAMA,
and Minoru SAITO

We propose a novel set of `representative' protein chains in PDB, where not only sequential but also structural similarities are taken into account.

Hobohm et al. have already proposed ``PDB_ SELECT'', which eliminates redundant chains based solely on sequence similarity. ``PDB_SELECT'' is frequently updated and the latest version is available at EMBL WWW server.

In our set of entries ``PDB-REPRDB,'' however, structural similarities are also considered, in order not to overlook local conformation diversity within a group of sequentially similar chains. Our set guarantees that every representative is the best among that similar protein group, regarding experimental or structure-determination quality (i.e. resolution and R-value).

The first version (based on PDB Release 70) of PDB-REPRDB was released in 1995 and the second version (PDB Release 78) will be available by April 1997.

Keywords: PDB (Protein Data Bank); representative protein chains;
sequential and structural similarity

Parallel Application Laboratory, Tsukuba Research Center
Real World Computing Partnership
Tsukuba Mitsui Bldg., 1-6-1 Takezono, Tsukuba 305, Japan
E-mail: noguchi@trc.rwcp.or.jp