PrimaDORAC：一个有机或药物分子中部分电荷、化学拓扑和键参数赋值的免费网络界面。
PrimaDORAC: A Free Web Interface for the Assignment of Partial Charges, Chemical Topology, and Bonded Parameters in Organic or Drug Molecules.
机构信息
Department of Chemistry, University of Florence , Via Lastruccia n.3, Sesto F.no, 50019, Italy.
出版信息
J Chem Inf Model. 2017 Jun 26;57(6):1240-1245. doi: 10.1021/acs.jcim.7b00145. Epub 2017 Jun 14.
UNLABELLED
We present PrimaDORAC, a simple and freely accessible web interface for generating the topology and the parameter files of organic or drug molecules to be used in molecular mechanics or molecular dynamics calculations. The interface relies on our in-house FORTRAN90 parser, working on the recently released Generalized Amber Force Field parameter set (GAFF2). AM1/BCC charges are computed using the Public Domain MOPAC7 program and the bond charge corrections (BCC) reported in Jakalian, A.; Jack, D. B.; Bayly, C. I.; J. Comp. Chem., 2002, 23, 1623-1641. The interface has been tested on about 52,000 compounds (identified with a CAS registry number) taken from the National Cancer Institute (NCI) Open Database. PrimaDORAC has been found to be very reliable, producing GAFF2 minimized structures bearing a mean root square displacement of about 0.01-0.02 nm with respect to the original CORINA-generated 3D NCI structures. As a demonstrative example, we release the full topology and parameter files, along with the AM1/BCC-GAFF2 computed in vacuo IR spectrum, for some recently discovered PARP/MCL1 inhibitors. The web interface and parser, including the sources, are part of the ORAC code (Procacci, P.; J. Chem. Inf.
MODEL
, 2016, 56, 1117-1121), distributed under the General Public License at www.chim.unifi.it/orac.
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我们提出了 PrimaDORAC，这是一个简单且可免费访问的网络界面，用于生成有机或药物分子的拓扑结构和参数文件，以用于分子力学或分子动力学计算。该界面依赖于我们内部的 FORTRAN90 解析器，使用最近发布的通用 Amber 力场参数集（GAFF2）。使用公共领域的 MOPAC7 程序和 Jakalian、A.；Jack、D. B.；Bayly、C. I. 报告的键电荷校正（BCC）计算 AM1/BCC 电荷，J. Comp. Chem.，2002，23，1623-1641。该界面已在大约 52000 种化合物（用 CAS 注册号标识）上进行了测试，这些化合物来自国家癌症研究所（NCI）开放数据库。PrimaDORAC 被发现非常可靠，生成的 GAFF2 最小化结构相对于原始 CORINA 生成的 3D NCI 结构的平均根均方位移约为 0.01-0.02nm。作为一个示范示例，我们发布了完整的拓扑结构和参数文件，以及在真空中计算的 AM1/BCC-GAFF2 的红外光谱，用于一些最近发现的 PARP/MCL1 抑制剂。该网络界面和解析器，包括源代码，都是 ORAC 代码（Procacci，P.；J. Chem. Inf. Model.，2016，56，1117-1121）的一部分，根据通用公共许可证在 www.chim.unifi.it/orac 上发布。
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