Improved scoring function for comparative modeling using the M4T method

Dmitry Rykunov, Elliot Steinberger, Carlos J. Madrid-Aliste, András Fiser

Research output: Contribution to journalArticlepeer-review

33 Scopus citations


Improvements in comparative protein structure modeling for the remote target-template sequence similarity cases are possible through the optimal combination of multiple template structures and by improving the quality of target-template alignment. Recently developed MMM and M4T methods were designed to address these problems. Here we describe new developments in both the alignment generation and the template selection parts of the modeling algorithms. We set up a new scoring function in MMM to deliver more accurate target-template alignments. This was achieved by developing and incorporating into the composite scoring function a novel statistical pairwise potential that combines local and non-local terms. The non-local term of the statistical potential utilizes a shuffled reference state definition that helped to eliminate most of the false positive signal from the background distribution of pairwise contacts. The accuracy of the scoring function was further increased by using BLOSUM mutation table scores.

Original languageEnglish (US)
Pages (from-to)95-99
Number of pages5
JournalJournal of Structural and Functional Genomics
Issue number1
StatePublished - Mar 2009


  • Comparative modeling
  • Homology modeling
  • Multiple mapping method
  • Target-template alignment
  • Template selection

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Genetics


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