PALI: a database of alignments and phylogeny of homologous protein structures
نویسندگان
چکیده
PALI is a database of structure-based sequence alignments and phylogenetic relationships derived on the basis of three-dimensional structures of homologous proteins. This database enables grouping of pairs of homologous protein structures on the basis of their sequence identity calculated from the structure-based alignment and PALI also enables association of a new sequence to a family and automatic generation of a dendrogram combining the query sequence and homologous protein structures.
منابع مشابه
PALI - a database of Phylogeny and ALIgnment of homologous protein structures
PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set comprises 604 families of homologous proteins involving 2739 protein domain struc...
متن کاملIntegration of related sequences with protein three-dimensional structural families in an updated version of PALI database
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...
متن کاملUse of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability among homologous proteins.
The database PALI (Phylogeny and ALIgnment of homologous protein structures) consists of families of protein domains of known three-dimensional (3D) structure. In a PALI family, every member has been structurally aligned with every other member (pairwise) and also simultaneous superposition (multiple) of all the members has been performed. The database also contains 3D structure-based and struc...
متن کاملSequencing and phylogenetic study of APETALA1 homologous gene in garden cress (Lepidium sativum L.)
The flowering process in plants proceeds through the induction of an inflorescence meristem triggered by several pathways. Many of the genes associated with these pathways encode transcription factors of the MADS domain family. The MADS-domain transcription factor APETALA1 (AP1) is a key regulator of flower development. The first step to understand the molecular mechanisms under the function of...
متن کاملSUPFAM - a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes
Members of a superfamily of proteins could result from divergent evolution of homologues with insignificant similarity in the amino acid sequences. A superfamily relationship is detected commonly after the three-dimensional structures of the proteins are determined using X-ray analysis or NMR. The SUPFAM database described here relates two homologous protein families in a multiple sequence alig...
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عنوان ژورنال:
- Bioinformatics
دوره 17 4 شماره
صفحات -
تاریخ انتشار 2001