Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys |
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Authors: | Dan M Bolser Ioannis Filippis Henning Stehr Jose Duarte Michael Lappe |
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Institution: | (1) The Max Planck Institute for Molecular Genetics, Berlin, Germany |
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Abstract: | Background For over 30 years potentials of mean force have been used to evaluate the relative energy of protein structures. The most
commonly used potentials define the energy of residue-residue interactions and are derived from the empirical analysis of
the known protein structures. However, single-body residue 'environment' potentials, although widely used in protein structure
analysis, have not been rigorously compared to these classical two-body residue-residue interaction potentials. Here we do
not try to combine the two different types of residue interaction potential, but rather to assess their independent contribution
to scoring protein structures. |
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Keywords: | |
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