Literature DB >> 19905480

Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations.

Daniel K Shenfeld1, Huafeng Xu, Michael P Eastwood, Ron O Dror, David E Shaw.   

Abstract

In computational thermodynamics, a sequence of intermediate states is commonly introduced to connect two equilibrium states. We consider two cases where the choice of intermediate states is particularly important: minimizing statistical error in free-energy difference calculations and maximizing average acceptance probabilities in replica-exchange simulations. We derive bounds for these quantities in terms of the thermodynamic distance between the intermediates, and show that in both cases the intermediates should be chosen as equidistant points along a geodesic connecting the end states.

Mesh:

Year:  2009        PMID: 19905480     DOI: 10.1103/PhysRevE.80.046705

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


  10 in total

1.  Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

Authors:  Jerome P Nilmeier; Gavin E Crooks; David D L Minh; John D Chodera
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-24       Impact factor: 11.205

2.  The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

Authors:  Andrea Rizzi; Travis Jensen; David R Slochower; Matteo Aldeghi; Vytautas Gapsys; Dimitris Ntekoumes; Stefano Bosisio; Michail Papadourakis; Niel M Henriksen; Bert L de Groot; Zoe Cournia; Alex Dickson; Julien Michel; Michael K Gilson; Michael R Shirts; David L Mobley; John D Chodera
Journal:  J Comput Aided Mol Des       Date:  2020-01-27       Impact factor: 3.686

3.  SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach.

Authors:  Piero Procacci; Massimiliano Guarrasi; Guido Guarnieri
Journal:  J Comput Aided Mol Des       Date:  2018-08-20       Impact factor: 3.686

Review 4.  Alchemical free energy methods for drug discovery: progress and challenges.

Authors:  John D Chodera; David L Mobley; Michael R Shirts; Richard W Dixon; Kim Branson; Vijay S Pande
Journal:  Curr Opin Struct Biol       Date:  2011-02-23       Impact factor: 6.809

5.  Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies.

Authors:  Si Zhang; David F Hahn; Michael R Shirts; Vincent A Voelz
Journal:  J Chem Theory Comput       Date:  2021-09-13       Impact factor: 6.578

6.  Optimal control of transitions between nonequilibrium steady states.

Authors:  Patrick R Zulkowski; David A Sivak; Michael R DeWeese
Journal:  PLoS One       Date:  2013-12-26       Impact factor: 3.240

7.  How does a small molecule bind at a cryptic binding site?

Authors:  Yibing Shan; Venkatesh P Mysore; Abba E Leffler; Eric T Kim; Shiori Sagawa; David E Shaw
Journal:  PLoS Comput Biol       Date:  2022-03-03       Impact factor: 4.475

8.  GAFF/IPolQ-Mod+LJ-Fit: Optimized force field parameters for solvation free energy predictions.

Authors:  Andreas Mecklenfeld; Gabriele Raabe
Journal:  ADMET DMPK       Date:  2020-06-28

9.  Theory of Adaptive Optimization for Umbrella Sampling.

Authors:  Soohyung Park; Wonpil Im
Journal:  J Chem Theory Comput       Date:  2014-06-12       Impact factor: 6.006

10.  Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.

Authors:  Mahmoud Moradi; Emad Tajkhorshid
Journal:  J Chem Theory Comput       Date:  2014-06-03       Impact factor: 6.006

  10 in total

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