Literature DB >> 22476552

The SAMPL3 blind prediction challenge: transfer energy overview.

Matthew T Geballe1, J Peter Guthrie.   

Abstract

Prediction of the free energy of solvation of a small molecule, or its transfer energy, is a necessary step along the path towards calculating the interactions between molecules that occur in an aqueous environment. A set of these transfer energies were gathered from the literature for series of chlorinated molecules with varying numbers of chlorines based on ethane, biphenyl, and dibenzo-p-dioxin. This focused set of molecules were then provided as a blinded challenge to assess the ability of current computational solvation methods to accurately model the interactions between water and increasingly chlorinated compounds. This was presented as part of the SAMPL3 challenge, which represented the fourth iterative blind prediction challenge involving transfer energies. The results of this exercise demonstrate that the field in general has difficulty predicting the transfer energies of more highly chlorinated compounds, and that methods seem to be erring in the same direction.

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Year:  2012        PMID: 22476552     DOI: 10.1007/s10822-012-9568-8

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


  8 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.  Automated server predictions in CASP7.

Authors:  James N D Battey; Jürgen Kopp; Lorenza Bordoli; Randy J Read; Neil D Clarke; Torsten Schwede
Journal:  Proteins       Date:  2007

3.  Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.

Authors:  Anthony Nicholls; David L Mobley; J Peter Guthrie; John D Chodera; Christopher I Bayly; Matthew D Cooper; Vijay S Pande
Journal:  J Med Chem       Date:  2008-01-24       Impact factor: 7.446

4.  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

5.  Predicting and measuring the solubility of p,p'- DDT in water.

Authors:  J W Biggar; G R Dutt; R L Riggs
Journal:  Bull Environ Contam Toxicol       Date:  1967-03       Impact factor: 2.151

Review 6.  Molecular recognition and binding free energy calculations in drug development.

Authors:  B N Dominy
Journal:  Curr Pharm Biotechnol       Date:  2008-04       Impact factor: 2.837

7.  Air-water Henry's law constants for PCB congeners: Experimental determination and modeling of structure-property relationship.

Authors:  Fu Fang; Shaogang Chu; Chia-Swee Hong
Journal:  Anal Chem       Date:  2006-08-01       Impact factor: 6.986

Review 8.  A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.

Authors:  John Moult
Journal:  Curr Opin Struct Biol       Date:  2005-06       Impact factor: 6.809

  8 in total
  37 in total

1.  Toward Learned Chemical Perception of Force Field Typing Rules.

Authors:  Camila Zanette; Caitlin C Bannan; Christopher I Bayly; Josh Fass; Michael K Gilson; Michael R Shirts; John D Chodera; David L Mobley
Journal:  J Chem Theory Comput       Date:  2018-12-24       Impact factor: 6.006

2.  SAMPL3: blinded prediction of host-guest binding affinities, hydration free energies, and trypsin inhibitors.

Authors:  A Geoffrey Skillman
Journal:  J Comput Aided Mol Des       Date:  2012-05-24       Impact factor: 3.686

3.  Prediction of free energies of hydration with COSMO-RS on the SAMPL3 data set.

Authors:  Jens Reinisch; Andreas Klamt; Michael Diedenhofen
Journal:  J Comput Aided Mol Des       Date:  2012-05-13       Impact factor: 3.686

4.  pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments.

Authors:  Mehtap Işık; Dorothy Levorse; Ariën S Rustenburg; Ikenna E Ndukwe; Heather Wang; Xiao Wang; Mikhail Reibarkh; Gary E Martin; Alexey A Makarov; David L Mobley; Timothy Rhodes; John D Chodera
Journal:  J Comput Aided Mol Des       Date:  2018-11-07       Impact factor: 3.686

5.  High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge.

Authors:  Philipp Pracht; Rainer Wilcken; Anikó Udvarhelyi; Stephane Rodde; Stefan Grimme
Journal:  J Comput Aided Mol Des       Date:  2018-08-23       Impact factor: 3.686

6.  Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge.

Authors:  Mehtap Işık; Dorothy Levorse; David L Mobley; Timothy Rhodes; John D Chodera
Journal:  J Comput Aided Mol Des       Date:  2019-12-19       Impact factor: 3.686

7.  An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge.

Authors:  Samarjeet Prasad; Jing Huang; Qiao Zeng; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2018-10-01       Impact factor: 3.686

8.  An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations.

Authors:  Frank C Pickard; Gerhard König; Andrew C Simmonett; Yihan Shao; Bernard R Brooks
Journal:  Bioorg Med Chem       Date:  2016-08-22       Impact factor: 3.641

9.  Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Authors:  David L Mobley; Caitlin C Bannan; Andrea Rizzi; Christopher I Bayly; John D Chodera; Victoria T Lim; Nathan M Lim; Kyle A Beauchamp; David R Slochower; Michael R Shirts; Michael K Gilson; Peter K Eastman
Journal:  J Chem Theory Comput       Date:  2018-10-30       Impact factor: 6.006

10.  Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.

Authors:  Gerhard König; Ye Mei; Frank C Pickard; Andrew C Simmonett; Benjamin T Miller; John M Herbert; H Lee Woodcock; Bernard R Brooks; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2015-12-11       Impact factor: 6.006

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