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

      Author(s): , , , , , , ,
      Publication date Created:
      Publication date (Print):
      Journal: Nature Methods
      Publisher: Springer Nature

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          Abstract

          An all-atom protein force field, CHARMM36m, offers improved accuracy for simulating intrinsically disordered peptides and proteins.

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          Comparison of simple potential functions for simulating liquid water

          William L Jorgensen, Jayaraman Chandrasekhar, Jeffry Madura … (1983)
          Article 0 comments Cited 3270 times – based on 0 reviews     Review now
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            Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

            Simon C. Lovell, Ian W. Davis, W Bryan Arendall … (2003)
            Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage). Copyright 2003 Wiley-Liss, Inc.
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              GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

              Berk Hess, Carsten Kutzner, David van der Spoel … (2008)
              Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.
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                Author and article information

                Journal
                Title: Nature Methods
                Abbreviated Title: Nat Meth
                Publisher: Springer Nature
                ISSN (Print): 1548-7091
                ISSN (Electronic): 1548-7105
                Publication date Created: November 7 2016
                Publication date (Print): November 7 2016
                Volume: 14
                Issue: 1
                Pages: 71-73
                Article
                DOI: 10.1038/nmeth.4067
                SO-VID: d17b5b85-942f-490d-8f42-8d1383c63d28
                Copyright © © 2016
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