Amino acid index databases

Figure 5.7. Amino acid index databases for physicochemical properties. The physicochemical properties, conformational parameters, and mutational indexes can be retrieved from AAindex database using keyword search.

Kawashima S, Ogata H, Kanehisa M. AAindex amino acid index database. Nucl. Acids Res. 1999 27 368-369. 

One of the most comprehensive resources of amino acid properties freely available on line is the amino acid index database (AAindex), which includes numerical indices representing various physico-chemical, biochemical, and statistical properties of amino acids and pairs of amino acids. AAindex database has been made publicly available by the Japanese GenomeNet database service (http //www.genome.jp/aaindex/). 

Physicochemical properties of amino acids are very useful descriptors for understanding the structures and properties of proteins. These properties are expressed numerically in indexes that can be retrieved from the AAindex database. Design an index database of physicochemical properties of amino acids with Microsoft Access that may facilitate the data retrieval according to their chemical similarities ... 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

From these databases, the atomic coordinates of fragments of three amino-acids matching the Xaa-Pro-Aro(0 sequence motif were extracted (t = index number of the aromatic residue). The sequences of the residue peptide fragments found in this way were mutated to Gly-Pro-Phe, in order to make comparison possible. For each peptide, the main-chain and side-chain dihedral angles, (J) / co Xjj, and all the proton chemical shifts were computed. Finally, the structures were clustered according to their backbone conformations and their computed chemical shifts. 

GeneSeq . Thomson Derwent s biosequence database, provides information on nucleic and amino acid sequences found in the patent literature. It has biosequence indexing for the patents included in the DWPI database beginning with the very first patents to carry protein and nucleotide sequence descriptions. GeneSeq structure searches retrieve records with the sequence, a short abstract directed to that sequence. 

The C-terminal amino acid residues preferred by TAP match with those generated by the proteolytic activities of the proteasome [23], as well as with C-terminal anchors used by most human class I molecules (database S YFPEITHI www.medizin.uni-tuebingen.de/ sfb510/index.html) [24]. 

Chemistry Index at Free University Berlin This is a collection of resources, many of them databases or files produced at FU Berlin. Included are files on Fundamental Physical Constants, Acronyms (with emphasis on chemistry and spectroscopy), and Amino Acids (arranged by name with the abbreviations and linear structural formulas). 

The WPIM file corresponds to Derwent World Patents Index (DWPI) online file, and therefore includes documents from all of the countries that Derwent normally covers. Indexing for WPIM began in 1987, and since 1987, Derwent has double indexed all chemical patents with both the fragmentation codes and WPIM indexing. Specific structures are indexed if they are not part of a Markush structure in the same patent document. Polymers are not indexed in detail in the WPIM database. Polypeptides of 10 or more amino acids are indexed in a separate non-Markush database and are not included in WPIM. All four online services that carry the DWPI also have the WPIM accession numbers. WPIM indexes patents from all countries in the Derwent database, but it is available to subscribers only. 

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