Blind prediction of solvation free energies from the SAMPL4 challenge.
Blind prediction of solvation free energies from the SAMPL4 challenge.
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DOI：
10.1007/s10822-014-9718-2
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发表时间：
2014-03
影响因子：
3.5
通讯作者：
Guthrie, J. Peter
中科院分区：
文献类型：
--
作者：
Mobley, David L.;Wymer, Karisa L.;Lim, Nathan M.;Guthrie, J. Peter
在这里，我们概述了SAMPL 4挑战的小分子水合部分，其重点是预测一系列47个小分子的水合自由能。这些气体到水的传递自由能在过去已经证明了各种计算方法和力场的有价值的测试。在这里，与之前的一些SAMPL挑战相比，我们发现相对广泛的方法在这个测试集上表现相当好，对于几种表现最好的方法，RMS误差在1.2 kcal/mol范围内。表现最好的包括量子力学方法与连续溶剂模型和官能团校正，炼金术分子动力学模拟与经典的全原子力场，和一个单一的conformation泊松-玻尔兹曼方法。虽然1.2 kcal/mol仍然是一个显著的误差，但实验水合自由能覆盖了近20 kcal/mol的范围，因此方法通常显示出相当大的预测能力。在这里，一个重要的新焦点是对误差估计的评估，因为预测计算预测何时可靠与不可靠具有相当大的实用价值。然而，我们发现，在许多情况下，错误被大大低估了，通常很少的努力已经投入到估计可能的错误。我们认为这是进一步研究的一个重要领域。
Here, we give an overview of the small molecule hydration portion of the SAMPL4 challenge, which focused on predicting hydration free energies for a series of 47 small molecules. These gas-to-water transfer free energies have in the past proven a valuable test of a variety of computational methods and force fields. Here, in contrast to some previous SAMPL challenges, we find a relatively wide range of methods perform quite well on this test set, with RMS errors in the 1.2 kcal/mol range for several of the best performing methods. Top-performers included a quantum mechanical approach with continuum solvent models and functional group corrections, alchemical molecular dynamics simulations with a classical all-atom force field, and a single-confor-mation Poisson-Boltzmann approach. While 1.2 kcal/mol is still a significant error, experimental hydration free energies covered a range of nearly 20 kcal/mol, so methods typically showed substantial predictive power. Here, a substantial new focus was on evaluation of error estimates, as predicting when a computational prediction is reliable vs. unreliable has considerable practical value. We found, however, that in many cases errors are substantially underestimated, and that typically little effort has been invested in estimating likely error. We believe this is an important area for further research.
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