Premium
A new soft‐core potential function for molecular dynamics applied to the prediction of protein loop conformations
Author(s) -
Tappura K.,
Lahtela–Kakkonen M.,
Teleman O.
Publication year - 2000
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(20000415)21:5<388::aid-jcc5>3.0.co;2-m
Subject(s) - molecular dynamics , loop (graph theory) , force field (fiction) , function (biology) , core (optical fiber) , biological system , chemistry , statistical physics , computational chemistry , computer science , chemical physics , physics , mathematics , artificial intelligence , biology , telecommunications , combinatorics , evolutionary biology
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. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 388–397, 2000