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Long-distance potentials: An approach to the multiple-minima problem in ligand-receptor interaction
Vakser, Ilya A.
Vakser, Ilya A.
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Abstract
The multiple-minima problem is a classical problem in molecular structure prediction. For ligand-receptor systems, a possible direction to alleviate this major obstacle is to simplify the objective function (intermolecular energy) and smooth its profile. We introduce long-distance atomatom potentials for ligand-receptor interactions. The longer ranges result in averaging of the energy potential at a given point. Our simplified force field is based on a trivial empirical representation of interatomic interactions as a step function. We demonstrate that the intermolecular energy calculation by a systematic search with such a simplified long-distance force field delivers the global minimum (crystallographically determined position of the ligand) by radically suppressing local minima (or false-positive fits). The effectiveness of the approach is demonstrated on different molecular complexes of known structure.
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This is the publisher's version, also available electronically from "http://peds.oxfordjournals.org/".
Date
1996-01-01
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Oxford University Press
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Vakser, I.A. (1996) Long-distance potentials: An approach to the multiple-minima problem in ligand-receptor interaction. Protein Eng., 9(1), 37-41. http://www.dx.doi.org/10.1093/protein/9.1.37