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Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database

Gowri, V S and Pandit, Shashi B and Karthik, P S and Srinivasan, N and Balaji, S (2003) Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. In: Nucleic Acids Research, 31 (1). pp. 486-488.

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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. The latest updated version (Release 2.1) comprises of 844 families of homologous proteins involving 3863 protein domain structures with each of these families having at least two members. Each member in a family has been structurally aligned with every other member in the same family using two proteins at a time. In addition, an alignment of multiple structures has also been performed using all the members in a family. Every family with at least three members is 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. 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.

Item Type: Journal Article
Publication: Nucleic Acids Research
Publisher: Oxford University Press
Additional Information: Copyright belongs to Oxford University Press.
Keywords: protein sequences;PALI;homologous proteins
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 04 Oct 2007
Last Modified: 19 Sep 2010 04:40
URI: http://eprints.iisc.ac.in/id/eprint/12084

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