Literature DB >> 11262940

Analyzing site heterogeneity during protein evolution.

J M Koshi1, R A Goldstein.   

Abstract

New computational models of the kinetics of natural site substitutions in proteins are described based on the underlying physical chemical properties of the amino acids. The corresponding reduction in the number of adjustable parameters allows us to analyze site-heterogeneity. Applying this evolutionary model to various data sets allows us to identify the important factors constraining molecular evolution, providing insight into the relationship between amino acid properties and protein structure.

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Year:  2001        PMID： 11262940     DOI： 10.1142/9789814447362_0020

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN： 2335-6928


  6 in total

1.  A mixed branch length model of heterotachy improves phylogenetic accuracy.

Authors:  Bryan Kolaczkowski; Joseph W Thornton
Journal:  Mol Biol Evol       Date:  2008-03-03       Impact factor: 16.240

2.  Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability.

Authors:  Miguel Arenas; Agustin Sánchez-Cobos; Ugo Bastolla
Journal:  Mol Biol Evol       Date:  2015-04-02       Impact factor: 16.240

3.  An HMM-based algorithm for evaluating rates of receptor-ligand binding kinetics from thermal fluctuation data.

Authors:  Lining Ju; Yijie Dylan Wang; Ying Hung; Chien-Fu Jeff Wu; Cheng Zhu
Journal:  Bioinformatics       Date:  2013-04-18       Impact factor: 6.937

4.  Using shifts in amino acid frequency and substitution rate to identify latent structural characters in base-excision repair enzymes.

Authors:  Ramiro Barrantes-Reynolds; Susan S Wallace; Jeffrey P Bond
Journal:  PLoS One       Date:  2011-10-06       Impact factor: 3.240

5.  Nonadaptive Amino Acid Convergence Rates Decrease over Time.

Authors:  Richard A Goldstein; Stephen T Pollard; Seena D Shah; David D Pollock
Journal:  Mol Biol Evol       Date:  2015-03-03       Impact factor: 16.240

6.  Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model.

Authors:  Nicolas Lartillot; Henner Brinkmann; Hervé Philippe
Journal:  BMC Evol Biol       Date:  2007-02-08       Impact factor: 3.260
  6 in total

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