Comment on “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes” | Zendy

Vytautas Gapsys | Zendy; Morteza Khabiri | Zendy; Bert L. de Groot | Zendy; Peter L. Freddolino | Zendy

Open Access

Comment on “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes”

Author(s) -

Vytautas Gapsys,

Morteza Khabiri,

Bert L. de Groot,

Peter L. Freddolino

Publication year - 2018

Publication title -

the journal of physical chemistry b

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.864

H-Index - 392

eISSN - 1520-6106

pISSN - 1520-5207

DOI - 10.1021/acs.jpcb.8b04187

Subject(s) - in silico , molecular dynamics , energy landscape , computational biology , transcription factor , computer science , dna binding site , statistical physics , biology , physics , chemistry , genetics , computational chemistry , gene , thermodynamics , promoter , gene expression

J. Phys. Chem. B 2017, 121 (20), 5151−5161, DOI: 10.1021/acs.jpcb.6b12450 A of May 18, 2018, the authors issue an Expression of Concern to advise readers of potential discrepancies between the results reported in this article and a recent, more successful, report of similar calculations (Gapsys and de Groot, JCTC 13:6275−6289 [DOI: 10.1021/acs.jctc.7b00849]). Based on the more recent publication, the authors now believe that technical shortcomings in the published calculations may underlie the poor agreements that were obtained between computed and experimental binding free energy profiles. The authors are in the process of investigating the likely sources of error, and the status of this article will be updated following the outcome of that investigation. Expression of Concern

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