Literature DB >> 27966363

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

Luke J Gosink, Christopher C Overall, Sarah M Reehl, Paul D Whitney, David L Mobley1, Nathan A Baker2.   

Abstract

This paper applies the Bayesian Model Averaging statistical ensemble technique to estimate small molecule solvation free energies. There is a wide range of methods available for predicting solvation free energies, ranging from empirical statistical models to ab initio quantum mechanical approaches. Each of these methods is based on a set of conceptual assumptions that can affect predictive accuracy and transferability. Using an iterative statistical process, we have selected and combined solvation energy estimates using an ensemble of 17 diverse methods from the fourth Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) blind prediction study to form a single, aggregated solvation energy estimate. Methods that possess minimal or redundant information are pruned from the ensemble and the evaluation process repeats until aggregate predictive performance can no longer be improved. We show that this process results in a final aggregate estimate that outperforms all individual methods by reducing estimate errors by as much as 91% to 1.2 kcal mol-1 accuracy. This work provides a new approach for accurate solvation free energy prediction and lays the foundation for future work on aggregate models that can balance computational cost with prediction accuracy.

Entities:  

Mesh:

Substances:

Year:  2017        PMID: 27966363      PMCID: PMC5398953          DOI: 10.1021/acs.jpcb.6b09198

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


  51 in total

1.  The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

Authors:  Emilio Gallicchio; Linda Yu Zhang; Ronald M Levy
Journal:  J Comput Chem       Date:  2002-04-15       Impact factor: 3.376

2.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

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

Authors:  Traian Sulea; Enrico O Purisima
Journal:  J Comput Aided Mol Des       Date:  2011-12-22       Impact factor: 3.686

4.  SAMPL2 and continuum modeling.

Authors:  Anthony Nicholls; Stanislaw Wlodek; J Andrew Grant
Journal:  J Comput Aided Mol Des       Date:  2010-04-06       Impact factor: 3.686

5.  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

6.  Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

Authors:  David L Mobley; Elise Dumont; John D Chodera; Ken A Dill
Journal:  J Phys Chem B       Date:  2007-02-10       Impact factor: 2.991

7.  An analysis of ensemble pruning techniques based on ordered aggregation.

Authors:  Gonzalo Martínez-Muñoz; Daniel Hernández-Lobato; Alberto Suárez
Journal:  IEEE Trans Pattern Anal Mach Intell       Date:  2009-02       Impact factor: 6.226

8.  Prediction of free energies of hydration with COSMO-RS on the SAMPL4 data set.

Authors:  Jens Reinisch; Andreas Klamt
Journal:  J Comput Aided Mol Des       Date:  2014-01-14       Impact factor: 3.686

Review 9.  Classical electrostatics in biology and chemistry.

Authors:  B Honig; A Nicholls
Journal:  Science       Date:  1995-05-26       Impact factor: 47.728

10.  Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models.

Authors:  Shina C L Kamerlin; Maciej Haranczyk; Arieh Warshel
Journal:  Chemphyschem       Date:  2009-05-11       Impact factor: 3.102

View more
  3 in total

1.  Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations.

Authors:  Xiu Yang; Huan Lei; Peiyuan Gao; Dennis G Thomas; David L Mobley; Nathan A Baker
Journal:  J Chem Theory Comput       Date:  2018-01-29       Impact factor: 6.006

2.  Validation of Free Energy Methods in AMBER.

Authors:  Hsu-Chun Tsai; Yujun Tao; Tai-Sung Lee; Kenneth M Merz; Darrin M York
Journal:  J Chem Inf Model       Date:  2020-07-06       Impact factor: 4.956

3.  An Immune-Gene-Based Classifier Predicts Prognosis in Patients With Cervical Squamous Cell Carcinoma.

Authors:  Huixia Yang; Xiaoyan Han; Zengping Hao
Journal:  Front Mol Biosci       Date:  2021-07-05
  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.