Literature DB >> 23066428

Recent Developments and Applications of the CHARMM force fields.

Xiao Zhu1, Pedro E M Lopes, Alexander D Mackerell.   

Abstract

Empirical force fields commonly used to describe the condensed phase properties of complex systems such as biological macromolecules are continuously being updated. Improvements in quantum mechanical (QM) methods used to generate target data, availability of new experimental target data, incorporation of new classes of compounds and new theoretical developments (eg. polarizable methods) make force-field development a dynamic domain of research. Accordingly, a number of improvements and extensions of the CHARMM force fields have occurred over the years. The objective of the present review is to provide an up-to-date overview of the CHARMM force fields. A limited presentation on the historical aspects of force fields will be given, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development. This is followed by information on the CHARMM additive and polarizable force fields, including examples of recent applications of those force fields.

Entities:  

Year:  2011        PMID: 23066428      PMCID: PMC3468154          DOI: 10.1002/wcms.74

Source DB:  PubMed          Journal:  Wiley Interdiscip Rev Comput Mol Sci        ISSN: 1759-0884


  75 in total

1.  2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonists.

Authors:  Denzil Bernard; Andrew Coop; Alexander D MacKerell
Journal:  J Am Chem Soc       Date:  2003-03-12       Impact factor: 15.419

2.  Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.

Authors:  Yongping Pan; Alexander D MacKerell
Journal:  Nucleic Acids Res       Date:  2003-12-15       Impact factor: 16.971

3.  An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Authors:  Jeffery B Klauda; Bernard R Brooks; Alexander D MacKerell; Richard M Venable; Richard W Pastor
Journal:  J Phys Chem B       Date:  2005-03-24       Impact factor: 2.991

4.  Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study.

Authors:  U Deva Priyakumar; Alexander D Mackerell
Journal:  J Phys Chem B       Date:  2008-01-16       Impact factor: 2.991

5.  Free energy profile of RNA hairpins: a molecular dynamics simulation study.

Authors:  Nan-Jie Deng; Piotr Cieplak
Journal:  Biophys J       Date:  2010-02-17       Impact factor: 4.033

6.  A revised potential-energy surface for molecular mechanics studies of carbohydrates.

Authors:  S N Ha; A Giammona; M Field; J W Brady
Journal:  Carbohydr Res       Date:  1988-09-15       Impact factor: 2.104

7.  Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

Authors:  Pär Bjelkmar; Per Larsson; Michel A Cuendet; Berk Hess; Erik Lindahl
Journal:  J Chem Theory Comput       Date:  2010-01-25       Impact factor: 6.006

Review 8.  Three-dimensional structures of oligosaccharides.

Authors:  R J Woods
Journal:  Curr Opin Struct Biol       Date:  1995-10       Impact factor: 6.809

9.  Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft.

Authors:  Olgun Guvench; Cheng-Kui Qu; Alexander D MacKerell
Journal:  BMC Struct Biol       Date:  2007-03-22

10.  Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations.

Authors:  Vineet Pande; Lennart Nilsson
Journal:  Nucleic Acids Res       Date:  2008-01-18       Impact factor: 16.971

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  49 in total

Review 1.  Force fields for simulating the interaction of surfaces with biological molecules.

Authors:  Lewis Martin; Marcela M Bilek; Anthony S Weiss; Serdar Kuyucak
Journal:  Interface Focus       Date:  2016-02-06       Impact factor: 3.906

2.  Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.

Authors:  Bin Lin; Pedro E M Lopes; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Phys       Date:  2013-08-28       Impact factor: 3.488

3.  Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.

Authors:  Fang-Yu Lin; Pedro E M Lopes; Edward Harder; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Inf Model       Date:  2018-04-17       Impact factor: 4.956

4.  All-atom MD indicates ion-dependent behavior of therapeutic DNA polymer.

Authors:  Ryan L Melvin; William H Gmeiner; Freddie R Salsbury
Journal:  Phys Chem Chem Phys       Date:  2017-08-23       Impact factor: 3.676

5.  Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation.

Authors:  Kevin R DeMarco; Slava Bekker; Igor Vorobyov
Journal:  J Physiol       Date:  2018-12-19       Impact factor: 5.182

6.  Six-site polarizable model of water based on the classical Drude oscillator.

Authors:  Wenbo Yu; Pedro E M Lopes; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Phys       Date:  2013-01-21       Impact factor: 3.488

7.  Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters.

Authors:  Aaron T Bozzi; Lukas B Bane; Wilhelm A Weihofen; Anne L McCabe; Abhishek Singharoy; Christophe J Chipot; Klaus Schulten; Rachelle Gaudet
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-29       Impact factor: 11.205

Review 8.  Molecular dynamics simulations in photosynthesis.

Authors:  Nicoletta Liguori; Roberta Croce; Siewert J Marrink; Sebastian Thallmair
Journal:  Photosynth Res       Date:  2020-04-15       Impact factor: 3.573

9.  Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field.

Authors:  Patric Schyman; William L Jorgensen
Journal:  J Phys Chem Lett       Date:  2013-01-17       Impact factor: 6.475

10.  A probabilistic approach for estimating water permeability in pressure-driven membranes.

Authors:  Linkel K Boateng; Ramin Madarshahian; Yeomin Yoon; Juan M Caicedo; Joseph R V Flora
Journal:  J Mol Model       Date:  2016-07-21       Impact factor: 1.810

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