Literature DB >> 27646287

Partition coefficients for the SAMPL5 challenge using transfer free energies.

Michael R Jones1,2, Bernard R Brooks2, Angela K Wilson3.   

Abstract

SAMPL challenges (Mobley et al. in J Comput Aided Mol Des 28:135-150, 2014; Skillman in J Comput Aided Mol Des 26:473-474, 2012; Geballe in J Comput Aided Mol Des 24:259-279, 2010; Guthrie in J Phys Chem B 113:4501-4507, 2009) provide excellent opportunities to assess theoretical approaches on new data sets with a goal of gaining greater insight towards protein and ligand modeling. In the SAMPL5 experiment, cyclohexane-water partition coefficients were determined using a vertical solvation scheme in conjunction with the SMD continuum solvent model. Several DFT functionals partnered with correlation consistent basis sets were evaluated for the prediction of the partition coefficients. The approach chosen for the competition, a B3PW91 vertical solvation scheme, yields a mean absolute deviation of 1.9 logP units and performs well at estimating the correct hydrophilicity and hydrophobicity for the full SAMPL5 molecule set.

Entities:  

Keywords:  B3PW91; Cyclohexane; DFT; Distribution coefficient; Partition coefficient; SAMPL; SMD; Solvation; Water

Mesh:

Substances:

Year:  2016        PMID: 27646287      PMCID: PMC6561331          DOI: 10.1007/s10822-016-9964-6

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


  37 in total

1.  The SAMPL2 blind prediction challenge: introduction and overview.

Authors:  Matthew T Geballe; A Geoffrey Skillman; Anthony Nicholls; J Peter Guthrie; Peter J Taylor
Journal:  J Comput Aided Mol Des       Date:  2010-05-09       Impact factor: 3.686

2.  Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions.

Authors:  Yan Zhao; Nathan E Schultz; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2006-03       Impact factor: 6.006

3.  Behavior of density functionals with respect to basis set. VI. Truncation of the correlation consistent basis sets.

Authors:  Brian P Prascher; Brent R Wilson; Angela K Wilson
Journal:  J Chem Phys       Date:  2007-09-28       Impact factor: 3.488

4.  General performance of density functionals.

Authors:  Sérgio Filipe Sousa; Pedro Alexandrino Fernandes; Maria João Ramos
Journal:  J Phys Chem A       Date:  2007-08-25       Impact factor: 2.781

5.  A blind challenge for computational solvation free energies: introduction and overview.

Authors:  J Peter Guthrie
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

6.  QSAR modeling: where have you been? Where are you going to?

Authors:  Artem Cherkasov; Eugene N Muratov; Denis Fourches; Alexandre Varnek; Igor I Baskin; Mark Cronin; John Dearden; Paola Gramatica; Yvonne C Martin; Roberto Todeschini; Viviana Consonni; Victor E Kuz'min; Richard Cramer; Romualdo Benigni; Chihae Yang; James Rathman; Lothar Terfloth; Johann Gasteiger; Ann Richard; Alexander Tropsha
Journal:  J Med Chem       Date:  2014-01-06       Impact factor: 7.446

Review 7.  LogD: lipophilicity for ionisable compounds.

Authors:  Melanie Kah; Colin D Brown
Journal:  Chemosphere       Date:  2008-06-18       Impact factor: 7.086

8.  Harmonic vibrational frequencies: scale factors for pure, hybrid, hybrid meta, and double-hybrid functionals in conjunction with correlation consistent basis sets.

Authors:  Marie L Laury; Scott E Boesch; Ian Haken; Pankaj Sinha; Ralph A Wheeler; Angela K Wilson
Journal:  J Comput Chem       Date:  2011-05-19       Impact factor: 3.376

Review 9.  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

10.  Performance of density functional theory for 3d transition metal-containing complexes: utilization of the correlation consistent basis sets.

Authors:  Sammer M Tekarli; Michael L Drummond; T Gavin Williams; Thomas R Cundari; Angela K Wilson
Journal:  J Phys Chem A       Date:  2009-07-30       Impact factor: 2.781

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  7 in total

1.  Benchmark of different charges for prediction of the partitioning coefficient through the hydrophilic/lipophilic index.

Authors:  Oksana Fizer; Maksym Fizer; Vasyl Sidey; Yaroslav Studenyak; Ruslan Mariychuk
Journal:  J Mol Model       Date:  2018-05-31       Impact factor: 1.810

2.  LogP prediction performance with the SMD solvation model and the M06 density functional family for SAMPL6 blind prediction challenge molecules.

Authors:  Davy Guan; Raymond Lui; Slade Matthews
Journal:  J Comput Aided Mol Des       Date:  2020-01-14       Impact factor: 3.686

3.  SAMPL6 logP challenge: machine learning and quantum mechanical approaches.

Authors:  Prajay Patel; David M Kuntz; Michael R Jones; Bernard R Brooks; Angela K Wilson
Journal:  J Comput Aided Mol Des       Date:  2020-01-30       Impact factor: 3.686

4.  Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields.

Authors:  Ye Ding; You Xu; Cheng Qian; Jinfeng Chen; Jian Zhu; Houhou Huang; Yi Shi; Jing Huang
Journal:  J Comput Aided Mol Des       Date:  2020-01-20       Impact factor: 3.686

5.  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

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

7.  Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge.

Authors:  Michael R Jones; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2020-01-30       Impact factor: 3.686

  7 in total

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