Literature DB >> 22190141

Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models.

Traian Sulea1, Enrico O Purisima.   

Abstract

Next-generation solvation models are devised to mimic the accuracy and generality of explicit solvation models at the speed of current popular implicit solvation models. One such method is the first-shell of hydration (FiSH) continuum model that was trained on hydration energetics from LIE calculations and molecular dynamics simulations in explicit solvent. Here we tested prospectively the FiSH model on the SAMPL-3 hydration data set that zooms in the effect of chlorination on solvation. We compare these FiSH predictions with those from retrospective LIE calculations. We find that neither FiSH nor LIE can reproduce well the absolute values and the trend of hydration free energies in the biphenyl and dioxin aromatic chlorination series. Some of the hypotheses behind this performance are discussed and tested. The LIE explicit-solvent model shows some improvement relative to the FiSH continuum model, and we correct a systematic deviation in the continuum van der Waals term of FiSH associated with aromatic Cl atom type.

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Year:  2011        PMID: 22190141     DOI: 10.1007/s10822-011-9522-1

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  27 in total

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Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

3.  Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations.

Authors:  Pavel V Klimovich; David L Mobley
Journal:  J Comput Aided Mol Des       Date:  2010-04-06       Impact factor: 3.686

4.  Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.

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Journal:  J Chem Theory Comput       Date:  2009-03-24       Impact factor: 6.006

5.  Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE).

Authors:  Traian Sulea; Christopher R Corbeil; Enrico O Purisima
Journal:  J Chem Theory Comput       Date:  2010-05-11       Impact factor: 6.006

6.  Surfaces affect ion pairing.

Authors:  Ilya Chorny; Ken A Dill; Matthew P Jacobson
Journal:  J Phys Chem B       Date:  2005-12-22       Impact factor: 2.991

7.  Charge asymmetries in hydration of polar solutes.

Authors:  David L Mobley; Janene R Baker; Alan E Barber; Christopher J Fennell; Ken A Dill
Journal:  J Phys Chem B       Date:  2008-02-06       Impact factor: 2.991

8.  Combination of RISM and Cheminformatics for Efficient Predictions of Hydration Free Energy of Polyfragment Molecules: Application to a Set of Organic Pollutants.

Authors:  Ekaterina L Ratkova; Maxim V Fedorov
Journal:  J Chem Theory Comput       Date:  2011-04-22       Impact factor: 6.006

9.  Predictions of hydration free energies from all-atom molecular dynamics simulations.

Authors:  David L Mobley; Christopher I Bayly; Matthew D Cooper; Ken A Dill
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

10.  How Can Hydrophobic Association Be Enthalpy Driven?

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Journal:  J Chem Theory Comput       Date:  2010-08-24       Impact factor: 6.006

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  4 in total

Review 1.  Blind prediction of solvation free energies from the SAMPL4 challenge.

Authors:  David L Mobley; Karisa L Wymer; Nathan M Lim; J Peter Guthrie
Journal:  J Comput Aided Mol Des       Date:  2014-03-11       Impact factor: 3.686

2.  Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method.

Authors:  Hervé Hogues; Traian Sulea; Francis Gaudreault; Christopher R Corbeil; Enrico O Purisima
Journal:  J Comput Aided Mol Des       Date:  2017-10-05       Impact factor: 3.686

3.  Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.

Authors:  Lauren Wickstrom; Nanjie Deng; Peng He; Ahmet Mentes; Crystal Nguyen; Michael K Gilson; Tom Kurtzman; Emilio Gallicchio; Ronald M Levy
Journal:  J Mol Recognit       Date:  2015-08-10       Impact factor: 2.137

4.  Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.

Authors:  Luke J Gosink; Christopher C Overall; Sarah M Reehl; Paul D Whitney; David L Mobley; Nathan A Baker
Journal:  J Phys Chem B       Date:  2017-01-04       Impact factor: 2.991

  4 in total

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