A new soft‐core potential function for molecular dynamics applied to the prediction of protein loop conformations

Kirsi Tappura (Corresponding Author), M. Lahtela-Kakkonen, Olle Teleman

    Research output: Contribution to journalArticleScientificpeer-review

    21 Citations (Scopus)

    Abstract

    We have developed a new soft‐core potential function for the conformational search of complex systems with molecular dynamics. The potential function was designed to maintain the main equilibrium properties of the original force field, which means that the soft‐core potential gives physically realistic performance also without additional restraints, different from most of the previous soft‐core potential functions. The performance of the method was demonstrated by applying it to the problem of finding native conformations for protein loops. Short loops from neocarzinostatin and parvalbumin were used as the first test cases. The use of the new soft‐core potential function was shown to improve significantly the performance of molecular dynamics in the search of the native conformation of protein loops.

    Original languageEnglish
    Pages (from-to)388 - 397
    Number of pages10
    JournalJournal of Computational Chemistry
    Volume21
    Issue number5
    DOIs
    Publication statusPublished - 2000
    MoE publication typeA1 Journal article-refereed

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