Literature DB >> 19281198

The SAMP1 solvation challenge: further lessons regarding the pitfalls of parametrization.

Anthony Nicholls1, Stanislaw Wlodek, J Andrew Grant.   

Abstract

This paper describes an investigation into the performance of different charges and radii with the Poisson-Boltzmann method for the calculation of vacuum-water transfer energies. The test set consisted of 63 drug-like molecules used in a blind-test challenge. The results are consistent with earlier reports, namely, that more physical charges perform better and that radii parametrization can both improve and also dramatically worsen results, with the latter suggesting a failure to capture all of the basic physics of solvation.

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Year:  2009        PMID: 19281198     DOI: 10.1021/jp806855q

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


  19 in total

1.  A very short history of structure-based design: how did we get here and where do we need to go?

Authors:  Jeff Blaney
Journal:  J Comput Aided Mol Des       Date:  2011-12-11       Impact factor: 3.686

2.  Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge.

Authors:  Enrico O Purisima; Christopher R Corbeil; Traian Sulea
Journal:  J Comput Aided Mol Des       Date:  2010-04-06       Impact factor: 3.686

3.  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

4.  Analysis of SM8 and Zap TK calculations and their geometric sensitivity.

Authors:  Benjamin A Ellingson; A Geoffrey Skillman; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2010-04-30       Impact factor: 3.686

5.  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

6.  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

7.  Predictions of hydration free energies from continuum solvent with solute polarizable models: the SAMPL2 blind challenge.

Authors:  Alexandre Meunier; Jean-François Truchon
Journal:  J Comput Aided Mol Des       Date:  2010-03-31       Impact factor: 3.686

8.  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

9.  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

10.  Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

Authors:  E V Katkova; A V Onufriev; B Aguilar; V B Sulimov
Journal:  J Mol Graph Model       Date:  2016-12-21       Impact factor: 2.518

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