Journal Article

Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction

Ilya A. Vakser

in Protein Engineering, Design and Selection

Volume 9, issue 1, pages 37-41
Published in print January 1996 | ISSN: 1741-0126
e-ISSN: 1741-0134 | DOI: https://dx.doi.org/10.1093/protein/9.1.37
Long-distance potentials: an approach to the multiple-minima problem in ligand-receptor interaction

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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.

Keywords: docking algorithms; drug design; energy minimization; molecular recognition; protein structure

Journal Article.  0 words. 

Subjects: Proteins

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