Literature DB >> 22060542

Approaching a parameter-free metadynamics.

Bradley M Dickson1.   

Abstract

We present a unique derivation of metadynamics. This work leads to a more robust understanding of the error in the computed free energy than what has been obtained previously. Moreover, a formula for the exact free energy is introduced. The formula can be used to post-process any existing well-tempered metadynamics data, allowing one, in principle, to obtain an exact free energy regardless of the metadynamics parameters.

Mesh：

Year:  2011        PMID： 22060542     DOI： 10.1103/PhysRevE.84.037701

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN： 1539-3755


  9 in total

1.  Using sketch-map coordinates to analyze and bias molecular dynamics simulations.

Authors:  Gareth A Tribello; Michele Ceriotti; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-16       Impact factor: 11.205

2.  Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents.

Authors:  Duy P Hua; He Huang; Amitava Roy; Carol Beth Post
Journal:  Protein Sci       Date:  2015-09-03       Impact factor: 6.725

3.  Unrestrained computation of free energy along a path.

Authors:  Bradley M Dickson; He Huang; Carol Beth Post
Journal:  J Phys Chem B       Date:  2012-08-30       Impact factor: 2.991

4.  All-atom adaptively biased path optimization of Src kinase conformational inactivation: Switched electrostatic network in the concerted motion of αC helix and the activation loop.

Authors:  Heng Wu; He Huang; Carol Beth Post
Journal:  J Chem Phys       Date:  2020-11-07       Impact factor: 3.488

5.  Optimal updating magnitude in adaptive flat-distribution sampling.

Authors:  Cheng Zhang; Justin A Drake; Jianpeng Ma; B Montgomery Pettitt
Journal:  J Chem Phys       Date:  2017-11-07       Impact factor: 3.488

6.  A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4.

Authors:  Bradley M Dickson; Parker W de Waal; Zachary H Ramjan; H Eric Xu; Scott B Rothbart
Journal:  J Chem Phys       Date:  2016-10-21       Impact factor: 3.488

7.  Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation.

Authors:  Scott B Rothbart; Bradley M Dickson; Michelle S Ong; Krzysztof Krajewski; Scott Houliston; Dmitri B Kireev; Cheryl H Arrowsmith; Brian D Strahl
Journal:  Genes Dev       Date:  2013-06-01       Impact factor: 11.361

8.  Molecular mechanisms of fentanyl mediated β-arrestin biased signaling.

Authors:  Parker W de Waal; Jingjing Shi; Erli You; Xiaoxi Wang; Karsten Melcher; Yi Jiang; H Eric Xu; Bradley M Dickson
Journal:  PLoS Comput Biol       Date:  2020-04-10       Impact factor: 4.475

9.  A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1.

Authors:  Jacob I Stuckey; Bradley M Dickson; Nancy Cheng; Yanli Liu; Jacqueline L Norris; Stephanie H Cholensky; Wolfram Tempel; Su Qin; Katherine G Huber; Cari Sagum; Karynne Black; Fengling Li; Xi-Ping Huang; Bryan L Roth; Brandi M Baughman; Guillermo Senisterra; Samantha G Pattenden; Masoud Vedadi; Peter J Brown; Mark T Bedford; Jinrong Min; Cheryl H Arrowsmith; Lindsey I James; Stephen V Frye
Journal:  Nat Chem Biol       Date:  2016-01-25       Impact factor: 15.040
  9 in total

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