Method for affinity scoring of peptide/protein complexes
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United States of America Patent
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Sep 17, 2013
Grant Date -
Nov 1, 2012
app pub date -
Oct 11, 2011
filing date -
Apr 21, 2004
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Abstract
The present invention is related to a quantitative structure-based affinity scoring method for peptide/protein complexes. More specifically, the present invention comprises a method that operates on the basis of a highly specific force field function (e.g. CHARMM) that is applied to all-atom structural representations of peptide/receptor complexes. Peptide side-chain contributions to total affinity are scored after detailed rotameric sampling followed by controlled energy refinement. The method of the invention further comprises a de novo approach to estimate dehydration energies from the simulation of individual amino acids in a solvent box filled with explicit water molecules and applying the same force field function as used to evaluate peptide/receptor complex interactions.
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