DBAli tools: mining the protein structure space

TitleDBAli tools: mining the protein structure space
Publication TypeJournal Article
Year of Publication2007
AuthorsMarti-Renom, MA, Pieper, U, Madhusudhan, MS, Rossi, A, Eswar, N, Davis, FP, Al-Shahrour, F, Dopazo, J, Sali, A
JournalNucleic Acids Res
Keywords*Algorithms Amino Acid Sequence Computational Biology/*methods Data Interpretation; Amino Acid *Software Structure-Activity Relationship; Protein Internet Molecular Sequence Data Protein Conformation Proteins/*chemistry/classification/*metabolism Pseudomonas aeruginosa/*metabolism Sequence Alignment/*methods Sequence Analysis; Protein/*methods Sequence Homology; Statistical *Databases

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.


Marti-Renom, Marc A Pieper, Ursula Madhusudhan, M S Rossi, Andrea Eswar, Narayanan Davis, Fred P Al-Shahrour, Fatima Dopazo, Joaquin Sali, Andrej GM 62529/GM/NIGMS NIH HHS/United States GM074929/GM/NIGMS NIH HHS/United States GM54762/GM/NIGMS NIH HHS/United States GM71790/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2007 Jul;35(Web Server issue):W393-7. Epub 2007 May 3.