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 structure-dependent sequence-based dendrograms [1,2]. The dataset of homologous protein structures used for the current release of PALI (version 2.6) has been obtained from the release 1.71 of the Structural Classification of Proteins (SCOP) database. There are 1664 multi-member families and 1239 orphans (single-member families) with 11,518 domains. Over 90,000 structural alignments (pairwise and multiple) have been generated for all multimember families. Every family with at least three members is associated with two dendrograms, one based on the structural dissimilarity metric defined for every pairwise rigid-body superposition and the other based on the similarity of topologically equivalent residues.For single member families, the sequences are available. Alignment of protein domains of known 3-D structure from PALI with the homologous sequences from the UniProt (Universal Protein Resource) database is 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 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 structures with best resolution have been represented as non-redundant entries for each family. Structure alignment program MUSTANG [3] has been used extensively to superimpose homologous protein domain structures.

GA and OK are supported by 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. V.S. Gowri, S.B. Pandit, P.S. Karthik, N. Srinivasan & S. Balaji (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. 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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