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Accuracy of current all-atom force-fields in modeling protein disordered states.
Journal article

Accuracy of current all-atom force-fields in modeling protein disordered states.

  • Palazzesi F Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich , CH-8093 Zurich, Switzerland.
  • Prakash MK Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur, Bangalore, Karnataka, 500064, India.
  • Bonomi M Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.
  • Barducci A Laboratoire de Biophysique Statistique, Ècole Polytechnique Fèdèrale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland.
  • 2015-11-18
Published in:
  • Journal of chemical theory and computation. - 2015
Molecular Dynamics Simulation
Nuclear Magnetic Resonance, Biomolecular
Protein Conformation
Proteins
English Molecular Dynamics (MD) plays a fundamental role in characterizing protein disordered states that are emerging as crucial actors in many biological processes. Here we assess the accuracy of three current force-fields in modeling disordered peptides by combining enhanced-sampling MD simulations with NMR data. These force-fields generate significantly different conformational ensembles, and AMBER03w [ Best and Mittal J. Phys. Chem. B 2010 , 114 , 14916 - 14923 ] provides the best agreement with experiments, which is further improved by adding the ILDN corrections [ Lindorff-Larsen et al. Proteins 2010 , 78 , 1950 - 1958 ].
Language
  • English
Open access status
closed
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Persistent URL
https://sonar.ch/global/documents/139775
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