AceDRG: a stereochemical description generator for ligands.
AceDRG: a stereochemical description generator for ligands.
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DOI：
10.1107/s2059798317000067
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发表时间：
2017-02-01
期刊：
影响因子：
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通讯作者：
Murshudov GN
中科院分区：
文献类型：
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作者：
Long F;Nicholls RA;Emsley P;Graǽulis S;Merkys A;Vaitkus A;Murshudov GN
AceDRG 程序可以生成给定配体的准确立体化学描述以及一种或多种构象。该程序还分析条目并从晶体学开放数据库中提取本地环境相关的原子类型、键和角度。 AceDRG 程序专为推导有关小分子的立体化学信息而设计。它使用基于局部化学和拓扑环境的原子分型来从小分子数据库：晶体学开放数据库 (COD) 中导出和组织键长和角度。有关原子杂化状态的信息、是否属于小环（最多七元环）、环芳香性和最近邻信息都编码在原子类型中。 COD 中的所有原子均已根据生成的原子类型进行了分类。所有键和角度也根据原子类型以及某种意义上的键类型进行分类。导出的数据以机器可读的形式制成表格，可从 CCP4 免费获取。如果配体的基本键合模式已知，AceDRG 还可以生成立体化学信息。基本键合模式是从一种计算化学文件格式中感知的，包括 SMILES、mmCIF、SDF MOL 和 SYBYL MOL2 文件。使用 COD 生成的键合化学、原子类型以及键和角度表，AceDRG 得出“理想”键长、角度、平面基团、芳香环和手性信息，并将它们写入 mmCIF 文件，可供细化程序 REFMAC5 和模型构建程序 Coot 使用。其他细化和模型构建程序（例如 PHENIX 和 BUSTER）也可以使用这些文件。 AceDRG 还生成与给定配体的最有利构象相对应的一个或多个坐标集。 AceDRG 使用 RDKit 进行化学感知和初始构象生成，以及 SMILES 字符串、SDF MOL 和 SYBYL MOL2 文件的解释。
The program AceDRG generates accurate stereochemical descriptions, and one or more conformations, of a given ligand. The program also analyses entries and extracts local environment-dependent atom types, bonds and angles from the Crystallography Open Database. The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the ‘ideal’ bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files.