NAR Molecular Biology Database Collection entry number 274

http://pauling.mbu.iisc.ernet.in/~pali

Agarwal G.¹, Krishnadev O.¹, Gowri V.S.¹, Srinivasan, N.¹, and Balaji S.¹

¹Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

Contact ns@mbu.iisc.ernet.in

The database of Phylogeny and ALIgnment of homologous protein structures (PALI) contains structure-based sequence alignments and dendrograms based on information derived from the alignments [1,2]. The dataset of homologous protein structures used for the current release of PALI (version 2.7) has been obtained from release 1.73 of the Structural Classification of Proteins (SCOP) database [3]. The structures with best resolution have been represented as non-redundant entries for each family. There are 1922 multimember families and 1433 orphans (single-member families) consisting of about 15,000 domains. Over 200,000 pairwise and 1922 multiple structural alignments have been generated for all multimember families. Each family with at least three members is associated with two dendrograms, one based on the structural dissimilarity metric defined for every pairwise superposition and the other based on the identity of the topologically equivalent residues. For single member families, the sequences are available. Alignments of protein domains of known 3-D structure from PALI integrated with homologous sequences from UniProt (Universal Protein Resource) database [4,5] are also available for every family in PALI. PSI-BLAST search using a query sequence can be performed against the structural members in PALI and also against the structural members integrated with the sequence homologues from the UniProt database. Search options for a query sequence using powerful procedures such as PSI-BLAST and RPS-BLAST are also available.

In the present version, the pairwise structural superposition has been generated using DALI[6,7]. Structure alignment program MUSTANG [8] has been used to superimpose multiple homologous protein domain structures.

RMB is supported by the Indian Institute of Science, Bangalore. GA and OK are supported by the Council of Scientific and Industrial Research, New Delhi. This work is supported by the Department of Biotechnology, New Delhi.

1. Balaji, S., Sujatha, S., Kumar, S.S.C., and Srinivasan, N. (2001) PALI: A database of Phylogeny and ALIgnment of homologous protein structures. Nucleic Acids Res. 29, 61-65.
2. Gowri, V.S., Pandit, S.B., Karthik, P.S., Srinivasan, N., and Balaji, S. (2003) Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database Nucleic Acids Res. 31, 486-488.
3. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
4. Apweiler, R,. Bairoch, A., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., et al. (2004) UniProt: the Universal Protein Knowledgebase. Nucleic Acids Res. 32, D115-D119.
5. Bairoch A., Apweiler R., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., et al.(2005) The Universal Protein Resource (UniProt). Nucleic Acids Res. 33, D154-159.
6. Holm L., and Sander C.(1996) Mapping the protein universe. Science 273, 595-602.
7. Holm L., an Park J.(2000) DaliLite workbench for structure comparison. Bioinformatics 16, 566-567.
8. Konagurthu A.S., Whisstock J.C., Stuckey P.J., Lesk A.M. (2006) MUSTANG: A multiple structural alignment algorithm.Proteins: Structure, Function and Bioinformatics. 64,559-574.

Go to the abstract in the NAR 2003 Database Issue.

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