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

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    VakserI_PE_9(1)37.pdf (459.3Kb)
    Issue Date
    1996-01-01
    Author
    Vakser, Ilya A.
    Publisher
    Oxford University Press
    Type
    Article
    Article Version
    Scholarly/refereed, publisher version
    Metadata
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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.
    Description
    This is the publisher's version, also available electronically from "http://peds.oxfordjournals.org/".
    URI
    http://hdl.handle.net/1808/17609
    DOI
    https://doi.org/10.1093/protein/9.1.37
    Collections
    • Molecular Biosciences Scholarly Works [526]
    Citation
    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

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    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

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