Journal Article

pdbFun: mass selection and fast comparison of annotated PDB residues

Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via and Manuela Helmer-Citterich

in Nucleic Acids Research

Volume 33, issue suppl_2, pages W133-W137
Published in print July 2005 | ISSN: 0305-1048
Published online July 2005 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/gki499

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pdbFun (http://pdbfun.uniroma2.it) is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. Users can select any residue subset (even including any number of PDB structures) by combining the available features. Selections can be used as probe and target in multiple structure comparison searches. For example a search could involve, as a query, all solvent-exposed, hydrophylic residues that are not in alpha-helices and are involved in nucleotide binding. Possible examples of targets are represented by another selection, a single structure or a dataset composed of many structures. The output is a list of aligned structural matches offered in tabular and also graphical format.

Journal Article.  2792 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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