Literature DB >> 21760975

Development of the CHARMM Force Field for Lipids.

R W Pastor1, A D Mackerell.   

Abstract

The development of the CHARMM additive all-atom lipid force field (FF) is traced from the early 1990's to the most recent version (C36) published in 2010. Though simulations with early versions yielded useful results, they failed to reproduce two important quantities: a zero surface tension at the experimental bilayer surface area, and the signature splitting of the deuterium order parameters in the glycerol and upper chain carbons. Systematic optimization of parameters based on high level quantum mechanical data and free energy simulations have resolved these issues, and bilayers with a wide range of lipids can be simulated in tensionless ensembles using C36. Issues associated with other all-atom lipid FFs, success and limitations in the C36 FF and ongoing developments are also discussed.

Entities:  

Year:  2011        PMID: 21760975      PMCID: PMC3133452          DOI: 10.1021/jz200167q

Source DB:  PubMed          Journal:  J Phys Chem Lett        ISSN: 1948-7185            Impact factor:   6.475


  35 in total

1.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

2.  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

3.  Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies.

Authors:  S E Feller; D Yin; R W Pastor; A D MacKerell
Journal:  Biophys J       Date:  1997-11       Impact factor: 4.033

Review 4.  The dipole potential of phospholipid membranes and methods for its detection.

Authors:  R J Clarke
Journal:  Adv Colloid Interface Sci       Date:  2001-01-29       Impact factor: 12.984

5.  Interaction of salicylate and a terpenoid plant extract with model membranes: reconciling experiments and simulations.

Authors:  Himanshu Khandelia; Sarah Witzke; Ole G Mouritsen
Journal:  Biophys J       Date:  2010-12-15       Impact factor: 4.033

6.  Comparison of the extended isotropic periodic sum and particle mesh Ewald methods for simulations of lipid bilayers and monolayers.

Authors:  Richard M Venable; Linda E Chen; Richard W Pastor
Journal:  J Phys Chem B       Date:  2009-04-30       Impact factor: 2.991

7.  CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.

Authors:  Elizabeth Hatcher; Olgun Guvench; Alexander D Mackerell
Journal:  J Phys Chem B       Date:  2009-09-17       Impact factor: 2.991

8.  CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Authors:  K Vanommeslaeghe; E Hatcher; C Acharya; S Kundu; S Zhong; J Shim; E Darian; O Guvench; P Lopes; I Vorobyov; A D Mackerell
Journal:  J Comput Chem       Date:  2010-03       Impact factor: 3.376

9.  Additive empirical force field for hexopyranose monosaccharides.

Authors:  Olgun Guvench; Shannon N Greene; Ganesh Kamath; John W Brady; Richard M Venable; Richard W Pastor; Alexander D Mackerell
Journal:  J Comput Chem       Date:  2008-11-30       Impact factor: 3.376

10.  Structure of Escherichia coli membranes. Glycerol auxotrophs as a tool for the analysis of the phospholipid head-group region by deuterium magentic resonance.

Authors:  H U Gally; G Pluschke; P Overath; J Seelig
Journal:  Biochemistry       Date:  1981-03-31       Impact factor: 3.162

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  85 in total

Review 1.  Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes.

Authors:  Jamie Parkin; Matthieu Chavent; Syma Khalid
Journal:  Biophys J       Date:  2015-08-04       Impact factor: 4.033

Review 2.  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

3.  Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions.

Authors:  M Gur; E Zomot; I Bahar
Journal:  J Chem Phys       Date:  2013-09-28       Impact factor: 3.488

4.  Physical chemistry and membrane properties of two phosphatidylinositol bisphosphate isomers.

Authors:  David R Slochower; Yu-Hsiu Wang; Ravi Radhakrishnan; Paul A Janmey
Journal:  Phys Chem Chem Phys       Date:  2015-05-21       Impact factor: 3.676

5.  All n-3 PUFA are not the same: MD simulations reveal differences in membrane organization for EPA, DHA and DPA.

Authors:  Xiaoling Leng; Jacob J Kinnun; Andres T Cavazos; Samuel W Canner; Saame Raza Shaikh; Scott E Feller; Stephen R Wassall
Journal:  Biochim Biophys Acta Biomembr       Date:  2018-01-03       Impact factor: 3.747

6.  Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.

Authors:  Hui Li; Janamejaya Chowdhary; Lei Huang; Xibing He; Alexander D MacKerell; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2017-08-08       Impact factor: 6.006

7.  Does the Lipid Bilayer Orchestrate Access and Binding of Ligands to Transmembrane Orthosteric/Allosteric Sites of G Protein-Coupled Receptors?

Authors:  Christopher T Szlenk; Jeevan B Gc; Senthil Natesan
Journal:  Mol Pharmacol       Date:  2019-04-08       Impact factor: 4.436

8.  A comparison of coarse-grained and continuum models for membrane bending in lipid bilayer fusion pores.

Authors:  Jejoong Yoo; Meyer B Jackson; Qiang Cui
Journal:  Biophys J       Date:  2013-02-19       Impact factor: 4.033

9.  Molecular dynamics simulations of lipid nanodiscs.

Authors:  Mohsen Pourmousa; Richard W Pastor
Journal:  Biochim Biophys Acta Biomembr       Date:  2018-05-03       Impact factor: 3.747

10.  Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics.

Authors:  Emilia L Wu; Olof Engström; Sunhwan Jo; Danielle Stuhlsatz; Min Sun Yeom; Jeffery B Klauda; Göran Widmalm; Wonpil Im
Journal:  Biophys J       Date:  2013-09-17       Impact factor: 4.033

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