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

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Volume

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Contents

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 SE- LECT," 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.