Improved scoring function for comparative modeling using the M4T method

  • Dmitry Rykunov
  • Elliot Steinberger
  • Carlos J. Madrid-Aliste
  • András FiserEmail author


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.


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



Multiple mapping method


Multiple mapping method with multiple templates



This work was supported by NIH GM62519-04. This work is dedicated to the memory of Elliot Steinberger, who passed away recently.


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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Dmitry Rykunov
    • 1
    • 2
  • Elliot Steinberger
    • 1
    • 2
  • Carlos J. Madrid-Aliste
    • 1
    • 2
  • András Fiser
    • 1
    • 2
    Email author
  1. 1.Department of Systems and Computational BiologyAlbert Einstein College of MedicineBronxUSA
  2. 2.Department of BiochemistryAlbert Einstein College of MedicineBronxUSA

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