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DBAli


NAR Molecular Biology Database Collection entry number 1169
Marti-Renom M.A.1, Pieper U.2, Eswar N.2, Webb B.2, Madhusudhan M.S.2, and Sali A.2
1Structural Genomics Unit, Bioinformatics Department. Centro de Investigación Príncipe Felipe. Valencia, Spain
2Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158-2330, USA
Contact mmarti@cipf.es

Database Description

DBAli, a database of pairwise and multiple structure alignments, stores pairwise comparisons of all structures in the Protein Data Bank calculated using the program MAMMOTH. It also contains multiple structure alignments generated by the SALIGN command of MODELLER. DBAli is updated weekly. As of August 2007, DBAli contains ~1.7 billion pairwise comparisons and over 12,500 family-based multiple structure alignments for ~35,000 non-redundant protein chains in the PDB.

Acknowledgements

We are grateful to Dr. Angel Ortiz for the MAMMOTH program. We would also like to thank the JMol team, Erik Bosrup, and Stijn van Dongen for JMol, overLib, and MCL, respectively. We appreciate valuable comments from Prof. Helen M. Berman, Prof. Wayne F. Anderson and several members of the Sali group, in particular Andrea Rossi and Fred P. Davis. AS acknowledge funding by The Sandler Family Supporting Foundation, NIH grants GM62529, GM74929, GM71790, and GM54762, as well as hardware gifts from Mike Homer, Ron Conway, IBM, Intel, HP, and NetApps. MAM-R acknowledges support from a Marie Curie International Reintegration Grant (FP6-039722) and the Generalitat Valenciana (GV/2007/065)

References

1. Marti-Renom, M.A., Pieper, U., Madhusudhan, M.S., Rossi, A., Eswar, N., Davis, F.P., Al-Shahrour, F., Dopazo, J. and Sali, A. (2007) DBAli tools: mining the protein structure space. Nucleic Acids Res, 35, W393-397.
2. Marti-Renom, M.A., Ilyin, V.A. and Sali, A. (2001) DBAli: a database of protein structure alignments. Bioinformatics, 17, 746-747.

Subcategory: Protein structure

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