Literature DB >> 18163606

Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations.

Julien Michel, Mario Orsi, Jonathan W Essex.   

Abstract

Coarse-grain models are becoming an increasingly important tool in computer simulations of a wide variety of molecular processes. In many instances it is, however, desirable to describe key portions of a molecular system at the atomic level. There is therefore a strong interest in the development of simulation methodologies that allow representations of matter with mixed granularities in a multiscale fashion. We report here a strategy to conduct mixed atomic-level and coarse-grain simulations of molecular systems with a recently developed coarse-grain model. The methodology is validated by computing partition coefficients of small molecules described in atomic detail and solvated by water or octane, both of which are represented by coarse-grain models. Because the present coarse-grain force field retains electrostatic interactions, the simplified solvent particles can interact realistically with the all-atom solutes. The partition coefficients computed by this approach rival the accuracy of fully atomistic simulations and are obtained at a fraction of their computational cost. The present methodology is simple, robust and applicable to a wide variety of molecular systems.

Entities:  

Year:  2007        PMID: 18163606     DOI: 10.1021/jp076142y

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  19 in total

Review 1.  Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations.

Authors:  Julien Michel; Jonathan W Essex
Journal:  J Comput Aided Mol Des       Date:  2010-05-28       Impact factor: 3.686

2.  Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.

Authors:  Caitlin C Bannan; Gaetano Calabró; Daisy Y Kyu; David L Mobley
Journal:  J Chem Theory Comput       Date:  2016-08-01       Impact factor: 6.006

3.  Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water.

Authors:  Xin Cindy Yan; Julian Tirado-Rives; William L Jorgensen
Journal:  J Phys Chem B       Date:  2016-03-01       Impact factor: 2.991

4.  Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations.

Authors:  Sereina Riniker; Andreas P Eichenberger; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2012-07-14       Impact factor: 1.733

5.  Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion.

Authors:  Timothy C Moore; Christopher R Iacovella; Clare McCabe
Journal:  J Chem Phys       Date:  2014-06-14       Impact factor: 3.488

6.  Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.

Authors:  Gerhard König; Frank C Pickard; Jing Huang; Andrew C Simmonett; Florentina Tofoleanu; Juyong Lee; Pavlo O Dral; Samarjeet Prasad; Michael Jones; Yihan Shao; Walter Thiel; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-08-30       Impact factor: 3.686

Review 7.  Adaptive resolution simulations of biomolecular systems.

Authors:  Julija Zavadlav; Staš Bevc; Matej Praprotnik
Journal:  Eur Biophys J       Date:  2017-09-13       Impact factor: 1.733

8.  Predicting octanol/water partition coefficients for the SAMPL6 challenge using the SM12, SM8, and SMD solvation models.

Authors:  Jonathan A Ouimet; Andrew S Paluch
Journal:  J Comput Aided Mol Des       Date:  2020-01-30       Impact factor: 3.686

9.  Hybrid coarse-graining approach for lipid bilayers at large length and time scales.

Authors:  Gary S Ayton; Gregory A Voth
Journal:  J Phys Chem B       Date:  2009-04-02       Impact factor: 2.991

10.  Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.

Authors:  Caitlin C Bannan; Kalistyn H Burley; Michael Chiu; Michael R Shirts; Michael K Gilson; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2016-09-27       Impact factor: 3.686

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