Research ArticleBIOCHEMISTRY

Blind protein structure prediction using accelerated free-energy simulations

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Science Advances  11 Nov 2016:
Vol. 2, no. 11, e1601274
DOI: 10.1126/sciadv.1601274

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Abstract

We report a key proof of principle of a new acceleration method [Modeling Employing Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It shows that such Boltzmann-satisfying techniques are now sufficiently fast and accurate to predict native protein structures in a limited test within the Critical Assessment of Structure Prediction (CASP) community-wide blind competition.

Keywords
  • Protein folding
  • structure prediction
  • molecular dynamics
  • replica exchange
  • simulations

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