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  1. PALI (View Publication)
    Full Name of the Resource : Phylogeny and alignment of homologous protein structures
    Resource Category : Databases -> Protein Sequence Databases -> Protein Domain Databases (Protein Classification)

    Brief Description : 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 2.8a) has been obtained from the release 1.75 of Structural Classification of Proteins (SCOP) database [3].The structures with best resolution have been represented as non-redundant entries for each family. There are 2058 multi-member families and 1716 orphans (single-member families) consisting of about 17,000 domains. Over 200,000 pairwise and 2058 multiple structural alignments 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 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 UniProt database. Search options for a query sequence using powerful procedures such as PSI-BLAST and RPS-BLAST are also available.
    Subject Area : Phyology; Homologous Protein


    Institute/s :
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Address of Institute/s :
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
    Country : India

    Associated Institutes :

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

    Associated Country : India


    Authors/Contributors : Srinivasan, N.
    Contact Email : ns@mbu.iisc.ernet.in
    Year : 2003
    Language : English

    Keywords : Databases, Factual; Internet; Phylogeny; Protein Structure, Quaternary; Proteins / chemistry / classification; Sequence Alignment