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PMID: 17478513 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

DBAli tools: mining the protein structure space.

Nucleic acids research ·Vol. 35 ·No. Web Server issue ·2007-07-00 ·Pages W393-7

Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A

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.

MeSH Terms
Algorithms Amino Acid Sequence Computational Biology/methods Data Interpretation, Statistical Databases, Protein Internet Molecular Sequence Data Protein Conformation Proteins/chemistry,classification,metabolism Pseudomonas aeruginosa/metabolism Sequence Alignment/methods Sequence Analysis, Protein/methods Sequence Homology, Amino Acid Software Structure-Activity Relationship
Chemicals
Proteins
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Marti-Renom Marc A
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
Pieper Ursula
Madhusudhan M S
Rossi Andrea
Eswar Narayanan
Davis Fred P
Al-Shahrour Fátima
Dopazo Joaquín
Sali Andrej
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkm236
Email
mmarti@cipf.es
Published
2007-07-00
Epub
2007-00-03
Pages
W393-7
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1933139
Subset
IM
Grants
NIGMS NIH HHS · P01 GM071790 · United States
NIGMS NIH HHS · P50 GM062529 · United States
NIGMS NIH HHS · R01 GM054762 · United States
NIGMS NIH HHS · GM074929 · United States
NIGMS NIH HHS · R29 GM054762 · United States
NIGMS NIH HHS · GM54762 · United States
NIGMS NIH HHS · GM 62529 · United States
NIGMS NIH HHS · U54 GM074929 · United States
NIGMS NIH HHS · GM71790 · United States
External Links
PubMed source DOI: 10.1093/nar/gkm236 PMC Full Text View journal details
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