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Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections
2016
Journal of Computer-Aided Molecular Design
Preserved Fulltext
Our free energy corrections based on QM protomer and pK a calculations increase the correlation between predicted and experimental distribution coefficients, for all methods used. ...
We present a protocol for accurately predicting partition coefficients between two immiscible phases, and then apply it to 53 druglike molecules in the SAMPL5 blind prediction challenge. ...
Acknowledgments This work was supported by the intramural research program of the National Heart, Lung and Blood Institute of the National Institutes of Health and utilized the high-performance computational ...
doi:10.1007/s10822-016-9955-7
pmid:27646286
fatcat:2uuv7e3r5zfifnq24ghozmscpq
Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge
2021
Journal of Computer-Aided Molecular Design
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The dataset was composed of a series of N-acylsulfonamides and related bioisosteres. 17 research groups participated in the log P challenge, submitting 33 blind submissions total. ...
Overall, the accuracy of octanol-water log P predictions in the SAMPL7 challenge was lower than octanol-water log P predictions in SAMPL6, likely due to a more diverse dataset. ...
TDB and DLM gratefully acknowledge support from NIH Grant R01GM124270 supporting the SAMPL Blind challenges. ...
doi:10.1007/s10822-021-00397-3
pmid:34169394
pmcid:PMC8224998
fatcat:foz35hwhzndmtmobdjkr7cdg6y
Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge
2016
Journal of Computer-Aided Molecular Design
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In the recent SAMPL5 challenge, participants submitted predictions for cyclohexane/water distribution coefficients for a set of 53 small molecules. ...
Distribution coefficients (log D) replace the hydration free energies that were a central part of the past five SAMPL challenges. ...
M.K.G. has an equity interest in and is a cofounder and scientific advisor of VeraChem LLC. ...
doi:10.1007/s10822-016-9954-8
pmid:27677750
pmcid:PMC5209301
fatcat:jywumgfy65ex3c2kzr7iboxzxu
An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations
2016
Bioorganic & Medicinal Chemistry
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Acknowledgments The authors would like to thank Tim Miller, Richard Venable and John Legato for technical assistance with the parallelization of the QM/MM calculations. ...
This work was supported by the intramural research program of the National Heart, Lung and Blood Institute of the National Institutes of Health and utilized the high-performance computational capabilities ...
We have applied this QM method together with the NBB free energy estimator in the recently completed SAMPL5 distribution coefficient challenge, Rustenburg et al. [2016] and strongly endorse it for making ...
doi:10.1016/j.bmc.2016.08.031
pmid:27667551
pmcid:PMC5068830
fatcat:aagocajwsnetvebe5zy6jwbhci
Octanol-water partition coefficient measurements for the SAMPL6 Blind Prediction Challenge
[article]
2019
bioRxiv
pre-print
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The SAMPL6 Part II Octanol-Water Partition Coefficient Prediction Challenge used a subset of kinase inhibitor fragment-like compounds from the SAMPL6 pKa Prediction Challenge in a blind experimental benchmark ...
The partition coefficient is a physicochemical property that captures the thermodynamics of relative solvation between aqueous and nonpolar phases, and therefore provides an excellent test for physics-based ...
Blind Prediction of Distribution in the SAMPL5 522 Challenge with QM Based Protomer and pKa Corrections. ...
doi:10.1101/757393
fatcat:odu45gvr55acvg6nvkn6ty4qom