FreeSolv: a database of experimental and calculated hydration free energies, with input files.
FreeSolv: a database of experimental and calculated hydration free energies, with input files.
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DOI：
10.1007/s10822-014-9747-x
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发表时间：
2014-07
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.;Guthrie, J. Peter
这项工作提供了水中中性小分子的实验和计算的水合自由能的精选数据库，以及分子结构、输入文件、参考文献和注释。我们称之为自由溶剂化数据库，或自由溶剂库。实验值取自以前的文献，并将继续进行整理，更新后的实验参考资料和数据将在可用时添加。计算值基于使用分子动力学模拟的炼金术自由能计算。采用了AM1-BCC电荷作用下的TIP3P水中的GAFF小分子力场。数值是用GROMACS模拟程序包计算的，在数据库本身引用的参考文献中给出了全部细节。这个数据库部分建立在先前包含类似信息的504个分子数据库的基础上。然而，这里已经对实验数据和计算值进行了额外的精选，分子总数现在达到了643个。其他信息现在包括在数据库中，如微笑字符串、PubChem复合ID、准确的参考DOI等。本文的支持信息中提供了数据库的一个版本，但随着不断更新的设想，数据库现在是在线版本和托管的。除了提供数据库之外，这项工作还描述了它的构建过程。该数据库可通过http://www.escholarship.org/uc/item/6sd403pz.免费使用
This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz.
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DOI：
10.1021/jp809782z
发表时间：
2009-05-14
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Fennell CJ;Bizjak A;Vlachy V;Dill KA
通讯作者：
Dill KA
影响因子：
5.5
作者：
Corbeil, Christopher R.;Sulea, Traian;Purisima, Enrico O.
通讯作者：
Purisima, Enrico O.
影响因子：
5.7
作者：
Liu, Yu;Fu, Jia;Wu, Jianzhong
通讯作者：
Wu, Jianzhong
影响因子：
3
作者：
Knight, Jennifer L.;Brooks, Charles L., III
通讯作者：
Brooks, Charles L., III
野外面：用于计算水中非极，极性和电荷溶质的溶剂化自由能的模型。
DOI：
10.1021/jp4115139
发表时间：
2014-06-19
期刊：
The journal of physical chemistry. B
影响因子：
--
作者：
Li L;Fennell CJ;Dill KA
通讯作者：
Dill KA