Mobley David L, Guthrie J Peter
Department of Pharmaceutical Sciences and Department of Chemistry, University of California, 147 Bison Modular, Irvine, CA, 92697, USA,
J Comput Aided Mol Des. 2014 Jul;28(7):711-20. doi: 10.1007/s10822-014-9747-x. Epub 2014 Jun 14.
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 .
这项工作提供了一个经过整理的数据库，其中包含水中小分子的实验和计算得到的水合自由能，以及分子结构、输入文件、参考文献和注释。我们将其称为自由溶剂化数据库，即FreeSolv。实验值取自先前的文献，并将持续进行整理，随着新的实验参考文献和数据的出现不断更新。计算值基于使用分子动力学模拟的炼金术自由能计算。这些计算使用了TIP3P水中的GAFF小分子力场和AM1-BCC电荷。使用GROMACS模拟软件包计算得到这些值，数据库本身引用的参考文献中给出了完整细节。该数据库部分基于之前一个包含类似信息的504个分子的数据库构建。然而，这里对实验数据和计算值都进行了额外的整理，分子总数现在达到了643个。数据库现在还包含了其他信息，如SMILES字符串、PubChem化合物ID、准确的参考文献DOI等。本文的支持信息中提供了数据库的一个版本，但由于预计会持续更新，该数据库现在进行了版本管理并在线托管。除了提供数据库外，这项工作还描述了其构建过程。该数据库可通过http://www.escholarship.org/uc/item/6sd403pz免费获取。
