Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge

Krämer Andreas; Hudson Phillip S.; Jones Michael R.Brooks Bernard R.

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Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge

机译：多相玻尔兹曼加权：在SAMPL6挑战中考虑水-辛醇分配系数分子模拟中的局部不均匀性

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titleAbstract/titlepAccurately computing partition coefficients is a pivotal part of drug discovery. Specifically, octanol–water partition coefficients can provide information into hydrophobicity of drug-like molecules, as well as a de facto representation of membrane permeability. However, one challenge facing the computation of partition coefficients is the need to encapsulate various microscopic environments. These include areas of largely bulk solvent (i.e., either water or octanol) or regions where octanol is saturated with water or areas of higher salt concentration. Also, tautomeric effects require consideration. Thus, we present a Boltzmann weighting approach that incorporates transfer free energies across varying microscopic media, as well as varying tautomeric state, to compute partition coefficients in the SAMPL6 challenge./p

机译：摘要准确计算分配系数是药物发现的关键部分。具体来说，辛醇-水分配系数可以提供药物样分子疏水性的信息，以及膜通透性的事实表示。然而，分配系数计算面临的一个挑战是需要封装各种微观环境。这些区域包括大量溶剂（即水或辛醇）的区域或辛醇被水饱和的区域或盐浓度较高的区域。此外，还需要考虑互变异构效应。因此，我们提出了一种玻尔兹曼加权方法，该方法结合了不同微观介质上的转移自由能以及不同的互变异构状态，以计算 SAMPL6 挑战中的分配系数。

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来源
《Journal of Computer-Aided Molecular Design》 |2020年第5期|471-483|共13页
作者
Krämer Andreas; Hudson Phillip S.; Jones Michael R.Brooks Bernard R.;
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作者单位

Laboratory of Computational Biology, National Heart, Lung and Blood Institute;

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原文格式 PDF
正文语种英语
中图分类电子计算机在化学中的应用;结构化学;
关键词
Alchemical simulation; Solvation free energy; Multi-phase; Boltzmann weighting; SAMPL6;

机译：炼金模拟;溶剂化自由能;多相;玻尔兹曼计权;SAMPL6的;

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1. Relationships Between Octanol/Water Partition Coefficients and Total Molecular Surface Area and Total Molecular Volume of Hydrophobic Organic Chemicals [J] . Jack de Bruijn, Joop Hermens Quantitative Structure-Activity Relationships: including Molecular Modelling and Applications of Computer Graphics in Pharmacology, Chemistry and Biology . 1990,第1期

机译：Relationships Between Octanol/Water Partition Coefficients and Total Molecular Surface Area and Total Molecular Volume of Hydrophobic Organic Chemicals
2. Prediction of n-octanol–water partition coefficient of platinum (IV) complexes using correlation weights of fragments of local symmetry [J] . Toropov Andrey A., Toropova Alla P., Achary P. Ganga Raju Structural Chemistry . 2023,第4期

机译：Prediction of n-octanol–water partition coefficient of platinum (IV) complexes using correlation weights of fragments of local symmetry
3. Correlation of Some Geometric Parameters Derived from Molecular Models of Monomer Nonionic Contrast Medium Molecules with Their Octanol/Water Partition Coefficient [J] . VIOLON DANIEL investigative radiology . 1996,第9期

机译：Correlation of Some Geometric Parameters Derived from Molecular Models of Monomer Nonionic Contrast Medium Molecules with Their Octanol/Water Partition Coefficient
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Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge

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