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Software on the evolution of protein structures

Software Index


It computes measures of the divergence in sequence and structure of homologous proteins with known structures and the corresponding pairwise violations of the molecular clock with respect to all possible outgroups.
Given a multiple sequence alignment, for all pairs of proteins it computes the Tajima-Nei sequence divergence, the contact divergence (Pascual-Garcia et al. 2010) and the TM-score (Zhang and Skolnick 2005) divergence -log(TM).
Input: alignment file in fasta format with names of pdb files as file names, optionally followed by the chain index (Ex: >1opd.pdb A). The first line may be PDBDIR= (default: current directory).
Output: File with pairwise divergences (optionally similarities) and file with pairwise violations of molecular clock for each divergence measure and corresponding significance.
  • Version: 1.0
  • License Free use for Educational and Research Purposes.
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  • References:
  • Pascual-García A, Arenas M, Bastolla U. The molecular clock in the evolution of protein structures. Mol Biol Evol, submitted (2017). [PDF]

    A. Pascual-Garcia; D. Abia; R. Méndez; G.S. Nido and U. Bastolla Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation. Proteins. 2010 78:181-96 . [Pubmed]

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