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Keywords:

  • threading;
  • protein structure prediction;
  • alignment;
  • twilight zone;
  • substitution matrix

Abstract

Recognizing the structural similarity without significant sequence identity (fold recognition) is an effective method for protein structure prediction. Previously, we developed a fold recognition potential called SORDIS, which incorporated side chain orientation in relation to hydrophobic core centers, distance of the residues from the protein globule center and secondary structure terms. But this potential does not include terms, based on close contacts between residues. In this paper a new fold recognition potential CONTSOR was presented, which based on SORDIS terms and the term, based on contacts between amino acid terminal groups. The performance of this potential was evaluated on SABmark benchmark for alignment accuracy and on SABmark and Lindahl benchmarks for fold recognition. The results show that CONTSOR has the best performance among other potentials on SABmark benchmark both for alignment accuracy and fold recognition and one of the best performances on Lindahl benchmark. CONTSOR software package is available for download at http://www.lifescience.org.ge/downloads/contsor.zip.