Cod-ConfDB: a codon - conformation database
A relational database of codons, corresponding amino acid sequence and the protein conformation in terms of dihedral angles, "Cod-ConfDB" has been developed considering well- resolved representative proteins of the protein data bank (PDB). In other words, the database provides information at three levels viz. the nucleotide level (codons), the protein primary structure level (amino acid sequence) and the three-dimensional structure level (conformation of the protein). The database is Web accessible and can be queried through the Web interface. The database would have numerous applications including the optimization of protein expression, serve as a knowledge base for proteinfolding algorithms and hence find application in protein three-dimensional structure prediction and further answering numerous questions such as the role of synonymous codons in fold determination etc.