Literature DB >> 24550133

Predicting hydration free energies with chemical accuracy: the SAMPL4 challenge.

Lars Sandberg1.   

Abstract

An implicit solvent model described by a non-simple dielectric medium is used for the prediction of hydration free energies on the dataset of 47 molecules in the SAMPL4 challenge. The solute is represented by a minimal parameter set model based on a new all atom force-field, named the liquid simulation force-field. The importance of a first solvation shell correction to the hydration free energy prediction is discussed and two different approaches are introduced to address it: either with an empirical correction to a few functional groups (alcohol, ether, ester, amines and aromatic nitrogen), or an ab initio correction based on the formation of a solute/explicit water complex. Both approaches give equally good predictions with an average unsigned error <1 kcal/mol. Chemical accuracy is obtained.

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Year:  2014        PMID: 24550133     DOI: 10.1007/s10822-014-9725-3

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


  5 in total

1.  A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums.

Authors:  Steven W Rick
Journal:  J Chem Phys       Date:  2004-04-01       Impact factor: 3.488

2.  Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods.

Authors:  Paulius Mikulskis; Samuel Genheden; Patrik Rydberg; Lars Sandberg; Lars Olsen; Ulf Ryde
Journal:  J Comput Aided Mol Des       Date:  2011-12-25       Impact factor: 3.686

Review 3.  Interfaces and the driving force of hydrophobic assembly.

Authors:  David Chandler
Journal:  Nature       Date:  2005-09-29       Impact factor: 49.962

4.  SAMPL4, a blind challenge for computational solvation free energies: the compounds considered.

Authors:  J Peter Guthrie
Journal:  J Comput Aided Mol Des       Date:  2014-04-06       Impact factor: 3.686

Review 5.  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

  5 in total
  6 in total

1.  Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile.

Authors:  Caroline C Zanith; Josefredo R Pliego
Journal:  J Comput Aided Mol Des       Date:  2014-11-15       Impact factor: 3.686

2.  Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK.

Authors:  Benjamin A Ellingson; Matthew T Geballe; Stanislaw Wlodek; Christopher I Bayly; A Geoffrey Skillman; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2014-03-16       Impact factor: 3.686

Review 3.  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

4.  Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Authors:  Juyong Lee; Florentina Tofoleanu; Frank C Pickard; Gerhard König; Jing Huang; Ana Damjanović; Minkyung Baek; Chaok Seok; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-09-27       Impact factor: 3.686

5.  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

6.  SAMPL7 blind challenge: quantum-mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules.

Authors:  Basak Koca Fındık; Zeynep Pinar Haslak; Evrim Arslan; Viktorya Aviyente
Journal:  J Comput Aided Mol Des       Date:  2021-06-24       Impact factor: 3.686

  6 in total

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