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Contact_divergence

  • Computes sequence and structure divergence measures of homologous proteins with known structures. 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).
  • Version: 1.0
  • Free use for Educational and Research Purposes.
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  • Reference: Pascual-García A, Abia D, Méndez R, Nido GS, Bastolla U. Proteins. 2010 78:181-96.
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