The molecular dynamics thermocycler. A new approach to sample conformational space, as exemplified by the RNA hairpin

The approach called the molecular dynamics thermocycler employs repeated cycles of heating and cooling of the model during the course of unrestrained in aqua MD simulation. It is validated by confronting results of three 1.6 ns simulations using different heating temperatures, starting from a de nov...

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Bibliographic Details
Published inNucleic Acids Symposium Series Vol. 2; no. 1; pp. 57 - 58
Main Authors Bielecki, Lukasz, Popenda, Mariusz, Adamiak, Ryszard W.
Format Journal Article
LanguageEnglish
Published Oxford University Press 01.11.2002
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Summary:The approach called the molecular dynamics thermocycler employs repeated cycles of heating and cooling of the model during the course of unrestrained in aqua MD simulation. It is validated by confronting results of three 1.6 ns simulations using different heating temperatures, starting from a de novo constructed 12-mer RNA hairpin model containing a UGAA loop vs. the set of NMR derived coordinates (PDB code 1AFX). The lowest average RMS deviation and best coherence with the experimentally delivered structures was identified in case of the molecular dynamics thermocycler using Tmax = 400 K.
ISSN:0261-3166
1746-8272
DOI:10.1093/nass/2.1.57