Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin

Proceedings of the National Academy of Sciences of the United States of America
Patrick ShafferMichele Parrinello

Abstract

The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin.

References

Dec 1, 1994·Journal of Computer-aided Molecular Design·T HuberW F van Gunsteren
Jun 29, 2000·Trends in Biochemical Sciences·A R DinnerM Karplus
Apr 6, 2001·Physical Review Letters·F Wang, D P Landau
Feb 28, 2002·Physical Review Letters·Ulrich H E Hansmann, Luc T Wille
Sep 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alessandro Laio, Michele Parrinello
Apr 6, 2004·Methods in Enzymology·Carol A RohlDavid Baker
Sep 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Pu LiuB J Berne
Feb 24, 2006·The Journal of Physical Chemistry. B·Paolo RaiteriMichele Parrinello
May 13, 2006·The Journal of Chemical Physics·Simon TrebstUlrich H E Hansmann
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Apr 11, 2007·The Journal of Physical Chemistry. B·Stefano Piana, Alessandro Laio
Feb 1, 2008·Physical Review Letters·Alessandro BarducciMichele Parrinello
Oct 28, 2008·Journal of the American Chemical Society·Shinya HondaKazuaki Harata
Mar 17, 2009·The Journal of Physical Chemistry. B·Paul MaragakisMartin Karplus
Nov 10, 2009·The Journal of Chemical Physics·Edina Rosta, Gerhard Hummer
Mar 3, 2010·Proceedings of the National Academy of Sciences of the United States of America·Cameron F Abrams, Eric Vanden-Eijnden
Sep 28, 2010·Physical Review Letters·M Bonomi, M Parrinello
Sep 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Gareth A TribelloMichele Parrinello
Mar 10, 2011·The Journal of Chemical Physics·Aviel Chaimovich, M Scott Shell
May 5, 2011·Biophysical Journal·Stefano PianaDavid E Shaw
Oct 29, 2011·Science·Kresten Lindorff-LarsenDavid E Shaw
Mar 5, 2013·Drug Discovery Today·Albert C PanDavid E Shaw
Jan 31, 2014·Physical Review Letters·Pratyush Tiwary, Michele Parrinello
Sep 13, 2014·Physical Review Letters·Omar Valsson, Michele Parrinello
Oct 1, 2014·Proceedings of the National Academy of Sciences of the United States of America·Susanne Gerber, Illia Horenko
Jan 22, 2015·Proceedings of the National Academy of Sciences of the United States of America·Pratyush TiwaryMichele Parrinello
Mar 5, 2015·Proceedings of the National Academy of Sciences of the United States of America·Ming ChenMark E Tuckerman
Apr 4, 2015·Journal of Chemical Theory and Computation·Alejandro Gil-Ley, Giovanni Bussi
May 20, 2015·The Journal of Physical Chemistry. B·Tong ZhangPhilippe Derreumaux
Jun 23, 2015·Journal of Computational Chemistry·Yinglong MiaoJ Andrew McCammon
Aug 4, 2015·The Journal of Chemical Physics·Jonathan K WhitmerJuan J de Pablo
Sep 1, 2015·Physical Review Letters·James McCartyMichele Parrinello
Nov 18, 2015·Journal of Chemical Theory and Computation·Jim Pfaendtner, Massimiliano Bonomi
Nov 18, 2015·Journal of Chemical Theory and Computation·Omar Valsson, Michele Parrinello
Jul 10, 2012·Journal of Chemical Theory and Computation·Michael DeighanJim Pfaendtner
Jul 12, 2011·Journal of Chemical Theory and Computation·Meher K PrakashMichele Parrinello
Mar 1, 2008·Journal of Chemical Theory and Computation·Berk HessErik Lindahl

❮ Previous
Next ❯

Citations

Apr 9, 2016·Journal of Chemical Theory and Computation·James McCartyMichele Parrinello
May 7, 2016·Journal of Chemical Theory and Computation·Alejandro Gil-LeyGiovanni Bussi
Mar 17, 2016·Annual Review of Physical Chemistry·Omar ValssonMichele Parrinello
Nov 5, 2016·Journal of Chemical Theory and Computation·Patrick ShafferMichele Parrinello
Feb 18, 2017·Journal of Chemical Theory and Computation·Christopher D FuJim Pfaendtner
Apr 25, 2017·Journal of Chemical Theory and Computation·Raimondas Galvelis, Yuji Sugita
May 31, 2017·Journal of Computational Chemistry·Ryuhei Harada, Yasuteru Shigeta
Dec 6, 2017·Physical Biology·Bozhi TianYuanwen Jiang
Aug 17, 2019·Proceedings of the National Academy of Sciences of the United States of America·Luigi BonatiMichele Parrinello
Aug 24, 2018·The Journal of Chemical Physics·João Marcelo Lamim RibeiroPratyush Tiwary
Mar 16, 2017·Proceedings of the National Academy of Sciences of the United States of America·Michele InvernizziMichele Parrinello
Feb 23, 2020·Proceedings. Mathematical, Physical, and Engineering Sciences·Z TrstanovaT Lelièvre
Nov 11, 2020·The Journal of Chemical Physics·Jun ZhangYi Qin Gao
Sep 15, 2017·The Journal of Physical Chemistry Letters·Ferruccio PalazzesiMichele Parrinello
Mar 20, 2020·The Journal of Physical Chemistry Letters·Michele Invernizzi, Michele Parrinello
Sep 17, 2019·The Journal of Physical Chemistry Letters·Jun ZhangFrank Noé
Sep 18, 2018·Journal of Chemical Theory and Computation·GiovanniMaria PicciniMichele Parrinello
May 2, 2018·Journal of Chemical Theory and Computation·Yi Isaac Yang, Michele Parrinello
Sep 30, 2021·The Journal of Physical Chemistry. B·Zachary Smith, Pratyush Tiwary

❮ Previous
Next ❯

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.

Related Papers

Journal of Neurology, Neurosurgery, and Psychiatry
C P Panayiotopoulos
Physical Review Letters
Pratyush Tiwary, Michele Parrinello
Developmental Medicine and Child Neurology
M C Bax
Hospital Management
A B COOK
© 2022 Meta ULC. All rights reserved