Literature DB >> 30074802

Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys.

Haohao Fu1, Hong Zhang1, Haochuan Chen1, Xueguang Shao1,2,3, Christophe Chipot4,5,6, Wensheng Cai1,2.   

Abstract

A robust importance-sampling algorithm for mapping free-energy surfaces over geometrical variables, coined meta-eABF, is introduced. This algorithm shaves the free-energy barriers and floods valleys by incorporating a history-dependent potential term in the extended adaptive biasing force (eABF) framework. Numerical applications on both toy models and nontrivial examples indicate that meta-eABF explores the free-energy surface significantly faster than either eABF or metadynamics (MtD) alone, without the need to stratify the reaction pathway. In some favorable cases, meta-eABF can be as much as five times faster than other importance-sampling algorithms. Many of the shortcomings inherent to eABF and MtD, like kinetic trapping in regions of configurational space already adequately sampled, the requirement of prior knowledge of the free-energy landscape to set up the simulation, are readily eliminated in meta-eABF. Meta-eABF, therefore, represents an appealing solution for a broad range of applications, especially when both eABF and MtD fail to achieve the desired result.

Year:  2018        PMID: 30074802     DOI: 10.1021/acs.jpclett.8b01994

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


  14 in total

1.  Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA.

Authors:  Dhiman Ray; Ioan Andricioaei
Journal:  Biophys J       Date:  2020-09-02       Impact factor: 4.033

2.  Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Authors:  James C Phillips; David J Hardy; Julio D C Maia; John E Stone; João V Ribeiro; Rafael C Bernardi; Ronak Buch; Giacomo Fiorin; Jérôme Hénin; Wei Jiang; Ryan McGreevy; Marcelo C R Melo; Brian K Radak; Robert D Skeel; Abhishek Singharoy; Yi Wang; Benoît Roux; Aleksei Aksimentiev; Zaida Luthey-Schulten; Laxmikant V Kalé; Klaus Schulten; Christophe Chipot; Emad Tajkhorshid
Journal:  J Chem Phys       Date:  2020-07-28       Impact factor: 3.488

3.  A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.

Authors:  Haochuan Chen; Dylan Ogden; Shashank Pant; Wensheng Cai; Emad Tajkhorshid; Mahmoud Moradi; Benoît Roux; Christophe Chipot
Journal:  J Chem Theory Comput       Date:  2022-02-09       Impact factor: 6.006

4.  Markov state models elucidate the stability of DNA influenced by the chiral 5S-Tg base.

Authors:  Shu-Dong Wang; Ru-Bo Zhang; Leif A Eriksson
Journal:  Nucleic Acids Res       Date:  2022-08-18       Impact factor: 19.160

Review 5.  Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations.

Authors:  Haohao Fu; Haochuan Chen; Marharyta Blazhynska; Emma Goulard Coderc de Lacam; Florence Szczepaniak; Anna Pavlova; Xueguang Shao; James C Gumbart; François Dehez; Benoît Roux; Wensheng Cai; Christophe Chipot
Journal:  Nat Protoc       Date:  2022-03-11       Impact factor: 17.021

6.  Human DNA Telomeres in Presence of Oxidative Lesions: The Crucial Role of Electrostatic Interactions on the Stability of Guanine Quadruplexes.

Authors:  Cecilia Hognon; Adrien Gebus; Giampaolo Barone; Antonio Monari
Journal:  Antioxidants (Basel)       Date:  2019-08-22

7.  Thermodynamics of Supramolecular Associations with Macrocyclic Water-Soluble Hosts.

Authors:  Ludovic Garnier; Christine Bonal; Patrice Malfreyt
Journal:  ACS Omega       Date:  2019-10-01

8.  Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond.

Authors:  Shu Dong Wang; Leif A Eriksson; Ru Bo Zhang
Journal:  J Chem Inf Model       Date:  2022-01-07       Impact factor: 4.956

9.  Potential of Matrix Metalloproteinase Inhibitors for the Treatment of Local Tissue Damage Induced by a Type P-I Snake Venom Metalloproteinase.

Authors:  Lina María Preciado; Jaime Andrés Pereañez; Jeffrey Comer
Journal:  Toxins (Basel)       Date:  2019-12-20       Impact factor: 4.546

Review 10.  Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches.

Authors:  Antonio Francés-Monerris; Cécilia Hognon; Tom Miclot; Cristina García-Iriepa; Isabel Iriepa; Alessio Terenzi; Stéphanie Grandemange; Giampaolo Barone; Marco Marazzi; Antonio Monari
Journal:  J Proteome Res       Date:  2020-10-29       Impact factor: 4.466

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