Go to the abstract in the NAR 2003 Database Issue.
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http://pauling.mbu.iisc.ernet.in/~pali
Gowri, V.S., Pandit, S.B., Karthik, P.S., Srinivasan, N., Balaji, S.
Molecular 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 three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of protein domains in various families (1,2). The latest updated version (Release 2.1) comprises of 844 families of homologous proteins, derived largely from SCOP (3) involving 3863 protein domain structures with each of these families having at least two members. Each member in a family has been structurally aligned to every other member in the same family and all the members in the family are also aligned simultaneously. Every family with at least three members is also associated with two dendrograms, one based on a structural dissimilarity metric and the other based on similarity of topologically equivalenced residues for every pairwise alignment. Apart from these multi-member families there are 817 single member families in the updated version of PALI. A new feature in the current release of PALI is the integration, with 3-D structural families, of sequences of homologues from the sequence databases (4). Alignments between homologous proteins of known 3-D structure and those without an experimentally derived structure are also provided for every family in the enhanced version of PALI. The database with several web interfaced utilities can be accessed at: http://pauling.mbu.iisc.ernet.in/~pali.
1. Significant increase in the size of the database in terms of number protein domains and number of structure-based alignments. 2a. Integration of structural families with sequence families. 2b. Multiple sequence alignment for every family that combines proteins from structural family and sequence family; availability of corresponding profiles. 3. Enhanced capability to match the query sequence with the profiles of PALI families using the profile-matching technique, IMPALA.
This research is supported by the Wellcome Trust, UK in terms of International Senior Fellowship to NS and Department of Biotechnology, India. SBP and SB are supported by the fellowships from CSIR, India.
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. Balaji, S., Sujatha, S., Aruna, S., Mhatre, N.S. & Srinivasan, N. (2002) PALI (Release 1.3) Nucleic Acids Res. http://www3.oup.co.uk/nar/database/summary/274
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. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Howe, K.L. and Sonnhammer, E.L.L. (2000) PFAM protein families database. Nucleic Acids Res., 28, 263-266.
Category Structure
Go to the abstract in the NAR 2003 Database Issue.