An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

Chemical Reviews
Justin A LemkulAlexander D MacKerell

Abstract

Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena.

References

Jun 16, 1977·Nature·J A McCammonM Karplus
Jun 8, 1978·Nature·W G HolH J Berendsen
Apr 20, 1991·Journal of Molecular Biology·T SimonsonG Bricogne
Apr 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·H R DrewR E Dickerson
Sep 6, 1994·Chemistry and Physics of Lipids·H BROCKMAN
Oct 1, 1996·Biophysical Journal·R L Baldwin
Feb 7, 1997·Science·J K GregoryR J Saykally
Mar 1, 1985·Physical Review A: General Physics·W G Hoover
Sep 15, 1988·Physical Review A: General Physics·A D Becke
Nov 25, 1985·Physical Review Letters·R Car, M Parrinello
Sep 25, 1999·Journal of Molecular Biology·T K ChiuR E Dickerson
Apr 13, 2000·Proceedings of the National Academy of Sciences of the United States of America·B F EichmanP S Ho
Apr 12, 2001·Current Opinion in Structural Biology·T A Halgren, W Damm
Mar 7, 2002·Proceedings of the National Academy of Sciences of the United States of America·Nicola G A AbresciaJuan A Subirana
Jun 19, 2002·Accounts of Chemical Research·Leonor Saiz, Michael L Klein
Oct 9, 2002·Journal of Computational Chemistry·D KonyW F Van Gunsteren
Oct 9, 2002·Journal of Computational Chemistry·Akihiro Morita
Oct 24, 2002·Journal of Computational Chemistry·Pengyu Ren, Jay W Ponder
Nov 25, 2003·Advances in Protein Chemistry·Jay W Ponder, David A Case
Nov 25, 2003·Journal of Computational Chemistry·Sandeep Patel, Charles L Brooks
Dec 20, 2003·Nature·Christopher M Dobson
Apr 7, 2004·Biochemistry·Nicola G A AbresciaJuan A Subirana
Jul 21, 2004·Journal of Computational Chemistry·Alexander D Mackerell
Mar 17, 2005·Journal of Computational Chemistry·Thereza A SoaresWilfred F van Gunsteren
May 5, 2005·Proceedings of the National Academy of Sciences of the United States of America·Richard A Friesner
May 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·A G DonchevV I Tarasov
Nov 5, 2005·The Journal of Chemical Physics·Timothy J Giese, Darrin M York
Jan 19, 2006·Journal of the American Chemical Society·U Deva Priyakumar, Alexander D Mackerell
Feb 24, 2006·The Journal of Physical Chemistry. B·Guillaume Lamoureux, Benoît Roux
Mar 15, 2006·Structure·Peter L FreddolinoKlaus Schulten
Mar 17, 2006·Current Opinion in Structural Biology·Patrice Koehl
Oct 1, 1952·Proceedings of the National Academy of Sciences of the United States of America·J G Kirkwood, J B Shumaker
May 26, 2006·Proceedings of the National Academy of Sciences of the United States of America·A G DonchevV I Tarasov

❮ Previous
Next ❯

Citations

Nov 3, 2016·The Journal of Chemical Physics·Andrew C SimmonettBernard R Brooks
Dec 29, 2016·Journal of Chemical Theory and Computation·Changsheng ZhangPengyu Ren
Jan 4, 2017·Chemical Reviews·Pengfei Li, Kenneth M Merz
Dec 20, 2016·The Journal of Physical Chemistry. B·Shu-Ching OuB Montgomery Pettitt
Feb 9, 2017·The Journal of Physical Chemistry Letters·Rui-Ning Sun, Haipeng Gong
Feb 9, 2017·Journal of Chemical Information and Modeling·Federico ZaharievMarilu Dick-Perez
Mar 18, 2017·The Journal of Physical Chemistry. B·Lee-Ping WangVijay S Pande
Apr 12, 2017·Journal of Chemical Theory and Computation·Justin A Lemkul, Alexander D MacKerell
May 10, 2017·Journal of Chemical Theory and Computation·Chengwen LiuPengyu Ren
May 17, 2017·The Journal of Physical Chemistry. B·Miaoren XiaDongqi Wang
May 11, 2017·Journal of Chemical Theory and Computation·Xi-Chan GaoChang-Sheng Wang
Jan 31, 2017·Journal of Computational Chemistry·Koen M VisscherDaan P Geerke
Mar 30, 2017·Physical Chemistry Chemical Physics : PCCP·Silvana PinheiroCarles Curutchet
Jul 22, 2017·Journal of Chemical Theory and Computation·Hui LiBenoît Roux
Jun 3, 2016·Physical Chemistry Chemical Physics : PCCP·David R BellPengyu Ren
Aug 18, 2017·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Timothy J Giese, Darrin M York
Mar 28, 2019·Annual Review of Biophysics·Zhifeng JingPengyu Ren
Sep 3, 2019·Physical Chemistry Chemical Physics : PCCP·Balasubramanian ChandramouliGiordano Mancini
Sep 14, 2019·Journal of Computational Chemistry·Fang-Yu Lin, Alexander D MacKerell
Nov 21, 2019·Journal of Computational Chemistry·Zak E HughesPaul L A Popelier
Dec 18, 2019·Journal of Computational Chemistry·Siddhartha LaghuvarapuU Deva Priyakumar
Mar 21, 2020·Physical Chemistry Chemical Physics : PCCP·Himanshu GoelAlexander D MacKerell
Jun 27, 2020·Physical Chemistry Chemical Physics : PCCP·Mattia BondanzaBenedetta Mennucci
Nov 20, 2016·Wiley Interdisciplinary Reviews. RNA·Jiří ŠponerMichal Otyepka
Nov 4, 2017·The Journal of Chemical Physics·Jing HuangBernard R Brooks
Nov 11, 2017·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Johannes ZemanChristian Holm
Oct 24, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Gerhard KönigDarrin M York
Jan 3, 2019·The Journal of Chemical Physics·Yifan Shen, Linjun Wang
Jan 19, 2019·Journal of Physics D: Applied Physics·Patricia BassereauThomas R Weikl
Aug 24, 2019·The Journal of Chemical Physics·Susmita GhoshSatyavani Vemparala
May 25, 2020·Journal of Molecular Modeling·Abhishek A KognoleAlexander D MacKerell
Sep 3, 2020·International Journal of Molecular Sciences·Veronika ZeindlhoferChristian Schröder
Sep 17, 2020·The Journal of Chemical Physics·Chang Yun Son, Zhen-Gang Wang
Feb 23, 2019·Soft Matter·Siva DasettySapna Sarupria
Dec 6, 2018·Journal of Computational Chemistry·Justin A Lemkul, Alexander D MacKerell
Nov 27, 2019·Physical Chemistry Chemical Physics : PCCP·Myong In OhDonald F Weaver

❮ Previous
Next ❯

Methods Mentioned

BETA
NMR
X-ray
protein folding

Software Mentioned

CGenFF
OpenMM
AMBER03
AMBER99SB
GROMACS
AMOEBA
POSSIM
NAMD
CHARMM36
AMBER

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.