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 manually-curated 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.