Literature DB >> 27819658

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

Jing Huang1, Sarah Rauscher2, Grzegorz Nawrocki3, Ting Ran1, Michael Feig3, Bert L de Groot2, Helmut Grubmüller2, Alexander D MacKerell1.   

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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Year:  2016        PMID： 27819658      PMCID： PMC5199616          DOI： 10.1038/nmeth.4067

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  36 in total

1.  Enhanced hairpin stability through loop design: the case of the protein G B1 domain hairpin.

Authors:  R Matthew Fesinmeyer; F Michael Hudson; Niels H Andersen
Journal:  J Am Chem Soc       Date:  2004-06-16       Impact factor: 15.419

2.  Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data.

Authors:  Athanasios S Baltzis; Nicholas M Glykos
Journal:  Protein Sci       Date:  2015-12-16       Impact factor: 6.725

Review 3.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

4.  Native like structure in the unfolded state of the villin headpiece helical subdomain, an ultrafast folding protein.

Authors:  Wenli Meng; Bing Shan; Yuefeng Tang; Daniel P Raleigh
Journal:  Protein Sci       Date:  2009-08       Impact factor: 6.725

5.  Testing the validity of ensemble descriptions of intrinsically disordered proteins.

Authors:  Malene Ringkjøbing Jensen; Martin Blackledge
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-17       Impact factor: 11.205

6.  Theoretically determined three-dimensional structure for the repeating tetrapeptide unit of the circumsporozoite coat protein of the malaria parasite Plasmodium falciparum.

Authors:  B R Brooks; R W Pastor; F W Carson
Journal:  Proc Natl Acad Sci U S A       Date:  1987-07       Impact factor: 11.205

7.  Polarizable empirical force field for alkanes based on the classical Drude oscillator model.

Authors:  Igor V Vorobyov; Victor M Anisimov; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2005-10-13       Impact factor: 2.991

Review 8.  Intrinsically disordered proteins in cellular signalling and regulation.

Authors:  Peter E Wright; H Jane Dyson
Journal:  Nat Rev Mol Cell Biol       Date:  2015-01       Impact factor: 94.444

9.  Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Authors:  Robert B Best; Xiao Zhu; Jihyun Shim; Pedro E M Lopes; Jeetain Mittal; Michael Feig; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2012-07-18       Impact factor: 6.006

10.  An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution.

Authors:  Aaron M Fluitt; Juan J de Pablo
Journal:  Biophys J       Date:  2015-09-01       Impact factor: 4.033
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  976 in total

1.  Toward Learned Chemical Perception of Force Field Typing Rules.

Authors:  Camila Zanette; Caitlin C Bannan; Christopher I Bayly; Josh Fass; Michael K Gilson; Michael R Shirts; John D Chodera; David L Mobley
Journal:  J Chem Theory Comput       Date:  2018-12-24       Impact factor: 6.006

2.  Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways.

Authors:  Johannes Hermann; Phillip Nowotny; Tobias E Schrader; Philipp Biggel; Dariusch Hekmat; Dirk Weuster-Botz
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2018-11-26       Impact factor: 1.056

3.  A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins.

Authors:  John J Ferrie; E James Petersson
Journal:  J Phys Chem B       Date:  2020-06-11       Impact factor: 2.991

4.  Structural Insights into the Lipid A Transport Pathway in MsbA.

Authors:  Pius S Padayatti; Sung Chang Lee; Robyn L Stanfield; Po-Chao Wen; Emad Tajkhorshid; Ian A Wilson; Qinghai Zhang
Journal:  Structure       Date:  2019-05-23       Impact factor: 5.006

5.  The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study.

Authors:  Chi-Jui Feng; Andrei Tokmakoff
Journal:  J Chem Phys       Date:  2017-08-28       Impact factor: 3.488

6.  Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.

Authors:  Fang-Yu Lin; Jing Huang; Poonam Pandey; Chetan Rupakheti; Jing Li; Benoı T Roux; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2020-04-27       Impact factor: 6.006

7.  PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer.

Authors:  Xingcheng Lin; Susmita Roy; Mohit Kumar Jolly; Federico Bocci; Nicholas P Schafer; Min-Yeh Tsai; Yihong Chen; Yanan He; Alexander Grishaev; Keith Weninger; John Orban; Prakash Kulkarni; Govindan Rangarajan; Herbert Levine; José N Onuchic
Journal:  J Mol Biol       Date:  2018-06-05       Impact factor: 5.469

8.  Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations.

Authors:  Wesley K Lay; Mark S Miller; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2017-04-28       Impact factor: 6.006

Review 9.  New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.

Authors:  Jejoong Yoo; Aleksei Aksimentiev
Journal:  Phys Chem Chem Phys       Date:  2018-03-28       Impact factor: 3.676

10.  Effect of Phosphorylation and O-GlcNAcylation on Proline-Rich Domains of Tau.

Authors:  Lata Rani; Jeetain Mittal; Sairam S Mallajosyula
Journal:  J Phys Chem B       Date:  2020-03-02       Impact factor: 2.991
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