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首页> 外文期刊>Acta crystallographica. Section D, Structural biology. >AceDRG AceDRG : a stereochemical description generator for ligands
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AceDRG AceDRG : a stereochemical description generator for ligands

机译：AceDRG AceDRG:立体化学的描述发电机为配体

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摘要

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 CCP 4. 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 REFMAC 5 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.
机译：程序AceDRG推导设计小的立体化学信息分子。基于原子类型推导和环境组织债券的长度和角度小分子数据库:应承担的结晶学开了数据库(COD)。杂化状态的原子,它们是否属于小环(7元环),芳香性和最近的邻居信息编码在原子类型。原子从鳕鱼已经分类显示生成的原子类型。根据原子也被分类类型,在某种意义上,债券类型。导出数据表在一个机器可读的从中共4形式,是免费的。也可以生成立体化学的信息,提供的基本键模式配体。计算化学的文件格式,包括微笑、mmCIF自卫队摩尔和SYBYL MOL2文件。化学、原子类型和债券和角表产生的鳕鱼,AceDRG派生的“理想”债券的长度、角度、平面组,芳香环和手性信息,写他们mmCIF文件,可以使用的细化项目REFMAC 5和模型构建程序傻瓜。如凤凰和和模型构建项目巴斯特还可以使用这些文件。生成一个或多个坐标集对应于最有利的构象(s)的配体。RDKit化学感知和初始构象的一代,以及微笑的解释字符串,自卫队摩尔SYBYL MOL2文件。

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