S L Samuel | PubMed Health

PubMed1991

Analysis of inverted repeats in primary structure of proteins.

A computer program has been developed to locate exact inverted repeating subsequences present anywhere in the given primary structure of proteins or nucleic acids. The output is amenable to protein sequence/nucleic acid query (PSQ/NAQ) packages. Our analysis has shown that there is a large number of proteins which have inverted repeats of more than four amino acid residues in length. However, the number is small when conditions such as the existence of more than 20 inverted repeats in given sequence or the existence of inverted repeats having more than five different types of amino acids are applied.

Amino Acid Sequence↗

PubMed1991

A protein secondary structure database (PSS).

A protein secondary structure database (PSS) has been designed to correlate the Protein Sequence Database of the PIR-International with the atomic coordinates and bond connectivities database of the Protein Data Bank in the Brookhaven National Laboratory. The present database includes secondary structures determined by X-ray diffraction analysis, but not predicted structures. The database currently contains data from both the Protein Sequence Database and the Protein Data Bank Database, and will encompass the NMR database in the future. The main characteristics of the database are as follows: (1) the secondary structures, sites, regions and domains of structural interest are displayed together with protein primary structures; and (2) the secondary structure of a desired length of peptide fragment is displayed upon request, as are the peptide fragment(s) that correspond to a defined secondary structure. This database also has software to indicate amino acid pairs having hydrogen bonds and to count the occurrence frequency of each pair as well as the conformational parameters widely used in semi-empirical methods of secondary structure prediction.

Amino Acid Sequence↗