AN INTEGRATED SEQUENCE-STRUCTURE DATABASE INCORPORATING MATCHING MESSENGER-RNA SEQUENCE, AMINO-ACID-SEQUENCE AND PROTEIN 3-DIMENSIONAL STRUCTURE DATA

We have constructed a non-homologous database, termed the Integrated S equence-Structure Database (ISSD) which comprises the coding sequences of genes, amino acid sequences of the corresponding proteins, their s econdary structure and phi, psi angles assignments, and polypeptide ba ckbone coordinates, Each protein entry in the database holds the align ment of nucleotide sequence, amino acid sequence and the PDB three-dim ensional structure data, The nucleotide and amino acid sequences for e ach entry are selected on the basis of exact matches of the source org anism and cell environment, The current version 1.0 of ISSD is availab le on the WWW at http://www.protein.bio.msu.su/issd/ and includes 107 non-homologous mammalian proteins, of which 80 are human proteins, The database has been used by us for the analysis of synonymous codon usa ge patterns in mRNA sequences showing their correlation with the three -dimensional structure features in the encoded proteins, Possible ISSD applications include optimisation of protein expression, improvement of the protein structure prediction accuracy, and analysis of evolutio nary aspects of the nucleotide sequence-protein structure relationship .