Literature DB >> 32786697

Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients.

Julia Gebhardt1, Matthias Kiesel1, Sereina Riniker2, Niels Hansen1.   

Abstract

Computational prediction of limiting activity coefficients is of great relevance for process design. For highly nonideal mixtures including molecules with directed interactions, methods that maintain the molecular character of the solvent are most promising. Computational expense and force-field deficiencies are the main limiting factors that prevent the use of high-throughput molecular dynamics (MD) simulations in a predictive setup. The combination of MD simulations and machine learning used in this work accounts for both issues. Comparison to published data including free-energy simulations, COSMO-RS and UNIFAC models, reveals competitive prediction accuracy.

Year:  2020        PMID: 32786697     DOI: 10.1021/acs.jcim.0c00479

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  3 in total

1.  Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning.

Authors:  John R Hamre; M Saleet Jafri
Journal:  Inform Med Unlocked       Date:  2022-02-28

Review 2.  From Data to Knowledge: Systematic Review of Tools for Automatic Analysis of Molecular Dynamics Output.

Authors:  Hanna Baltrukevich; Sabina Podlewska
Journal:  Front Pharmacol       Date:  2022-03-10       Impact factor: 5.810

3.  Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers.

Authors:  Agastya P Bhati; Shunzhou Wan; Dario Alfè; Austin R Clyde; Mathis Bode; Li Tan; Mikhail Titov; Andre Merzky; Matteo Turilli; Shantenu Jha; Roger R Highfield; Walter Rocchia; Nicola Scafuri; Sauro Succi; Dieter Kranzlmüller; Gerald Mathias; David Wifling; Yann Donon; Alberto Di Meglio; Sofia Vallecorsa; Heng Ma; Anda Trifan; Arvind Ramanathan; Tom Brettin; Alexander Partin; Fangfang Xia; Xiaotan Duan; Rick Stevens; Peter V Coveney
Journal:  Interface Focus       Date:  2021-10-12       Impact factor: 3.906

  3 in total

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