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Literature DB >> 25330958

Current status of protein force fields for molecular dynamics simulations.

Pedro E M Lopes¹, Olgun Guvench, Alexander D MacKerell.

Abstract

The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields.

Entities: Chemical Disease Gene

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Year: 2015 PMID： 25330958 PMCID： PMC4554537 DOI： 10.1007/978-1-4939-1465-4_3

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

84 in total

1. Ion solvation thermodynamics from simulation with a polarizable force field.

Authors: Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal: J Am Chem Soc Date: 2003-12-17 Impact factor: 15.419

Review 2. Force fields for protein simulations.

Authors: Jay W Ponder; David A Case
Journal: Adv Protein Chem Date: 2003

3. Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator.

Authors: Edward Harder; Victor M Anisimov; Igor V Vorobyov; Pedro E M Lopes; Sergei Y Noskov; Alexander D MacKerell; Benoît Roux
Journal: J Chem Theory Comput Date: 2006-11 Impact factor: 6.006

4. Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.

Authors: Igor Vorobyov; Victor M Anisimov; Shannon Greene; Richard M Venable; Adam Moser; Richard W Pastor; Alexander D MacKerell
Journal: J Chem Theory Comput Date: 2007-05 Impact factor: 6.006

5. Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study.

Authors: Jürgen Graf; Phuong H Nguyen; Gerhard Stock; Harald Schwalbe
Journal: J Am Chem Soc Date: 2007-02-07 Impact factor: 15.419

6. Recent Developments and Applications of the CHARMM force fields.

Authors: Xiao Zhu; Pedro E M Lopes; Alexander D Mackerell
Journal: Wiley Interdiscip Rev Comput Mol Sci Date: 2011-06-28

7. 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

8. The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

Authors: Yue Shi; Zhen Xia; Jiajing Zhang; Robert Best; Chuanjie Wu; Jay W Ponder; Pengyu Ren
Journal: J Chem Theory Comput Date: 2013 Impact factor: 6.006

9. (Ala)(4)-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters.

Authors: Jihyun Shim; Xiao Zhu; Robert B Best; Alexander D MacKerell
Journal: J Comput Chem Date: 2012-11-29 Impact factor: 3.376

10. Improved side-chain torsion potentials for the Amber ff99SB protein force field.

Authors: Kresten Lindorff-Larsen; Stefano Piana; Kim Palmo; Paul Maragakis; John L Klepeis; Ron O Dror; David E Shaw
Journal: Proteins Date: 2010-06

32 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. Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88.

Authors: Juan Zeng; Yongxiu Li; John Z H Zhang; Ye Mei
Journal: J Mol Model Date: 2016-07-08 Impact factor: 1.810

3. AMOEBA+ Classical Potential for Modeling Molecular Interactions.

Authors: Chengwen Liu; Jean-Philip Piquemal; Pengyu Ren
Journal: J Chem Theory Comput Date: 2019-06-11 Impact factor: 6.006

4. Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides.

Authors: Christina E Faller; Olgun Guvench
Journal: J Phys Chem B Date: 2015-05-07 Impact factor: 2.991

Review 5. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors: A T Hagler
Journal: J Comput Aided Mol Des Date: 2018-11-30 Impact factor: 3.686

Review 6. Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?

Authors: Pnina Dauber-Osguthorpe; A T Hagler
Journal: J Comput Aided Mol Des Date: 2018-11-30 Impact factor: 3.686