CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins

By Jing Huang, Sarah Rauscher, G. Nawrocki, T. Ran, Michael Feig, B. L. de Groot, Helmut Grubmüller, A. MacKerell. 2016

6,170 citations recorded by the source corpus.

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.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Evolutionary context-integrated deep sequence modeling for protein engineering (2020, background): “Rational design is oftentimes assisted by quantitative approaches to evaluate sequences that fold into a specific structure, including biophysical modeling [3,4] , force field approximations [5–7] , structure prediction [8–10] , and molecular dynamics simulations [11] .”
Driven to Near-Experimental Accuracy by Refinement via Molecular Dynamics Simulations (2019, methodology): “For the iterative protocol, MD simulations were conducted with flat-bottom harmonic restraints and a modified version of the CHARMM 36 m force field 34 with explicit water molecules.”
AlphaFold2 models indicate that protein sequence determines both structure and dynamics (2022, methodology): “The protein atoms were typed according to the CHARMM force field 38,39 (c36m) and a modified TIP3P model 40 was used for the solvent water molecules.”
CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates (2019, methodology): “MD simulations of a fully glycosylated HIV envelope trimer (from PDB:5FYL or using Glycan Modeler) were performed using the CHARMM36m force field (Huang et al. 2017) and NAMD 2.”
Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification (2017, methodology): “12 package (52) with the CHARMM36m force field and the CMAP backbone energy correction (53).”
Shape shifting: The multiple conformational substates of the PTEN N‐terminal PIP2 ‐binding domain (2022, methodology): “2 software(67) with CHARMM36m forcefield.(68) The MD simulations were analyzed utilizing the GROMOS clustering algorithm,(69) inter-residue CONtact ANalysis (CONAN),(42) Residue Interaction Network (RIN) analysis,(70) and residual local frustration analysis.”
8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI (2022, methodology): “All simulations were performed using CHARMM36m forcefields (Huang et al., 2017).”