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CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Nature Methods volume 14, pages 7173 (2017) | Download Citation

Abstract

The all-atom additive CHARMM36 protein force field is widely used in molecular modeling and simulations. We present its refinement, CHARMM36m (http://mackerell.umaryland.edu/charmm_ff.shtml), with improved accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins.

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Acknowledgements

Financial support from the NIH (GM072558 to A.D.M.) and (GM084953 to M.F.) and computational support from the University of Maryland Computer-Aided Drug Design Center, XSEDE (TG-MCA98N017 to A.D.M.) and (TG-MCB090003 to M.F.) and the SuperMUC supercomputer at the Leibniz Rechenzentrum in Garching provided through an allocation by the Gauss Supercomputing Center to S.R. and H.G. are acknowledged. We thank V. Gapsys for helpful discussions. S.R. is supported by a postdoctoral fellowship from the Alexander von Humboldt Foundation.

Author information

Affiliations

  1. Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA.

    • Jing Huang
    • , Ting Ran
    •  & Alexander D MacKerell Jr
  2. Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

    • Sarah Rauscher
    • , Bert L de Groot
    •  & Helmut Grubmüller
  3. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.

    • Grzegorz Nawrocki
    •  & Michael Feig

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Contributions

J.H. performed the force field optimization. J.H., S.R., G.N. and M.F. ran simulations. J.H., S.R., G.N., T.R. and M.F. analyzed data. J.H., S.R., M.F., B.L.d.G., H.G. and A.D.M. wrote the manuscript. A.D.M. conceived and initiated the research.

Competing interests

A.D.M. is cofounder and CSO of SilcsBio LLC.

Corresponding author

Correspondence to Alexander D MacKerell Jr.

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    Supplementary Text and Figures

    Supplementary Figures 1–20, Supplementary Tables 1–18 and Supplementary Note.

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DOI

https://doi.org/10.1038/nmeth.4067

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