Literature DB >> 11301310

PALI: a database of alignments and phylogeny of homologous protein structures.

S Sujatha1, S Balaji, N Srinivasan.   

Abstract

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.

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Year:  2001        PMID： 11301310     DOI： 10.1093/bioinformatics/17.4.375

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  7 in total

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

Authors:  V S Gowri; Shashi B Pandit; P S Karthik; N Srinivasan; S Balaji
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

2.  Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution.

Authors:  S Balaji; N Srinivasan
Journal:  J Biosci       Date:  2007-01       Impact factor: 1.826

3.  Alignment of multiple protein structures based on sequence and structure features.

Authors:  M S Madhusudhan; Benjamin M Webb; Marc A Marti-Renom; Narayanan Eswar; Andrej Sali
Journal:  Protein Eng Des Sel       Date:  2009-07-08       Impact factor: 1.650

4.  Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding.

Authors:  Qi-Shi Du; Dong Chen; Neng-Zhong Xie; Ri-Bo Huang; Kuo-Chen Chou
Journal:  J Biomol Struct Dyn       Date:  2014-12-22

5.  Local structural differences in homologous proteins: specificities in different SCOP classes.

Authors:  Agnel Praveen Joseph; Hélène Valadié; Narayanaswamy Srinivasan; Alexandre G de Brevern
Journal:  PLoS One       Date:  2012-06-22       Impact factor: 3.240

6.  Accuracy of structure-based sequence alignment of automatic methods.

Authors:  Changhoon Kim; Byungkook Lee
Journal:  BMC Bioinformatics       Date:  2007-09-20       Impact factor: 3.169

7.  An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data.

Authors:  Jianbo Lu; Guoliang Xu; Shihua Zhang; Benzhuo Lu
Journal:  Algorithms Mol Biol       Date:  2016-06-21       Impact factor: 1.405
  7 in total

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