An integrated database for complex protein structure modeling

In homology modeling of protein structures, it is typical to find templates through a sequence search against a database of proteins with known structures. In more complicated modeling cases, such as modeling a protein structure in contact with a ligand, sequence information itself may not be enough and more biological information is required for a successful modeling process. SCOP and PFAM are two databases providing protein domain information which can be utilized in complex protein structure modeling. However, due to the manuallycurated nature of both databases, they fail to provide timely coverage of protein sequences existing in the Protein Data Bank (PDB). In this paper, we introduce a new relational database, IDOPS, which integrates sequence and biological information extracted from remediated PDB files and protein domain information generated with HMM profiles of PFAM families. With a carefully designed protocol, this database is updated regularly and the coverage rate of PDB entries is guaranteed to be high.