The solvated interaction energy method for scoring binding affinities

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DOIResolve DOI: http://doi.org/10.1007/978-1-61779-465-0_19
AuthorSearch for: ; Search for:
TypeArticle
Journal titleComputational Drug Discovery and Design
Series titleMethods in Molecular Biology; Volume 819
ISBN978-1-61779-464-3
Pages295303; # of pages: 9
Subjectbinding free energy; scoring function; protein-ligand binding; molecular dynamics
AbstractThe solvated interaction energy (SIE) is an end-point, physics-based scoring function for predicting ligand-binding affinities. It supplements the force-field interaction energy with the desolvation cost of binding. Parameters such as the solute dielectric constant, Born radii, a cavity term and an overall scaling coefficient and additive constant have been previously calibrated against a training set of 99 protein–ligand complexes. We describe the application of the method to estimating binding free energies from molecular dynamics trajectories of protein–ligand binding complexes.
Publication date
PublisherSpringer
LanguageEnglish
AffiliationNRC Biotechnology Research Institute; National Research Council Canada
Peer reviewedYes
NRC number53202
NPARC number21268278
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Record identifiera9f3d349-72f5-4a79-845e-0967dd29c44b
Record created2013-06-13
Record modified2016-05-09
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