title: DBAli tools: mining the protein structure space.
abstract: The DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB). These tools include (i) the DBAlit program that allows users to input the 3D coordinates of a protein structure for comparison by MAMMOTH against all chains in the PDB; (ii) the AnnoLite and AnnoLyze programs that annotate a target structure based on its stored relationships to other structures; (iii) the ModClus program that clusters structures by sequence and structure similarities; (iv) the ModDom program that identifies domains as recurrent structural fragments and (v) an implementation of the COMPARER method in the SALIGN command in MODELLER that creates a multiple structure alignment for a set of related protein structures. Thus, the DBAli tools, which are freely accessible via the World Wide Web at http://salilab.org/DBAli/, allow users to mine the protein structure space by establishing relationships between protein structures and their functions.
authors.affiliation: Structural Genomics Unit, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158-2330, USA. mmarti@cipf.es
authors.forename: Marc A
authors.initials: MA
authors.lastname: Marti-Renom
authors.forename: Ursula
authors.initials: U
authors.lastname: Pieper
authors.forename: M S
authors.initials: MS
authors.lastname: Madhusudhan
authors.forename: Andrea
authors.initials: A
authors.lastname: Rossi
authors.forename: Narayanan
authors.initials: N
authors.lastname: Eswar
authors.forename: Fred P
authors.initials: FP
authors.lastname: Davis
authors.forename: Fátima
authors.initials: F
authors.lastname: Al-Shahrour
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D020407:Internet; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D011550:Pseudomonas aeruginosa / Q000378:metabolism*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins