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

20 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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Potential Function
Conformation
Molecular Dynamics
Conformations
Molecular dynamics
Proteins
Protein
Prediction
Zinostatin
Parvalbumins
Force Field
Large scale systems
Complex Systems

Cite this

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A new soft‐core potential function for molecular dynamics applied to the prediction of protein loop conformations. / Tappura, Kirsi (Corresponding Author); Lahtela-Kakkonen, M.; Teleman, Olle.

In: Journal of Computational Chemistry, Vol. 21, No. 5, 2000, p. 388 - 397.

Research output: Contribution to journalArticleScientificpeer-review

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