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Distance dependent centroid to centroid force fields using high resolution decoys.

Distance dependent centroid to centroid force fields using high resolution decoys. Research Abstract Details 

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  • Distance dependent centroid to centroid force fields using high resolution decoys. Abstract Text:

    r rajgariaR Rajgaria,s r mcallisterS R McAllister,c a floudasC A Floudas,

    Simplified force fields play an important role in protein structure prediction and de novo protein design by requiring less computational effort than detailed atomistic potentials. A side chain centroid based, distance dependent pairwise interaction potential has been developed. A linear programming based formulation was used in which non-native "decoy" conformers are forced to take a higher energy compared with the corresponding native structure. This model was trained on an enhanced and diverse protein set. High quality decoy structures were generated for approximately 1400 nonhomologous proteins using torsion angle dynamics along with restricted variations of the hydrophobic cores of the native structure. The resulting decoy set was used to train the model yielding two different side chain centroid based force fields that differ in the way distance dependence has been used to calculate energy parameters. These force fields were tested on an independent set of 148 test proteins with 500 decoy structures for each protein. The side chain centroid force fields were successful in correctly identifying approximately 86% native structures. The Z-scores produced by the proposed centroid-centroid distance dependent force fields improved compared with other distance dependent C(alpha)-C(alpha) or side chain based force fields.

    Distance dependent centroid to centroid force fields using high resolution decoys. Publishing Authors By Initials

    r rajgariaR Rajgaria,sr mcallisterSR McAllister,ca floudasCA Floudas,

    For similar abstracts research abstracts see: abstracts research

    PUBMED ID PMID:

    MEDLINE DATE:

    Distance dependent centroid to centroid force fields using high resolution decoys. Journal Published:

    PUBLICATION TYPE: Research Support, U.S. Gov't,

    Journal: Proteins

    VOLUME: 70

    Page Numbers: 950-70

    Journal Abbreviation: Proteins

    ISSN: 1097-0134

    DAY: 15

    MONTH: Feb

    YEAR: 2008

    Distance dependent centroid to centroid force fields using high resolution decoys. Information

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    LANGUAGE: eng

    NlmUniqueID: 8700181

    Distance dependent centroid to centroid force fields using high resolution decoys. Keywords Mesh Terms:

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    Grant and Affiliation Information for Distance dependent centroid to centroid force fields using high resolution decoys.

    AFFILIATION: Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544-5263, USA.

    Country: United States

    United States Research PublicationUnited States Research Publication

    AGENCY: United States NIGMS

    GRANT: R24 GM069736

    ACRONYM: GM

    MEDLINETA: Proteins

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