JLigand: a graphical tool for the CCP4 template-restraint library.
JLigand: a graphical tool for the CCP4 template-restraint library.
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DOI：
10.1107/s090744491200251x
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发表时间：
2012-04
期刊：
影响因子：
--
通讯作者：
Murshudov GN
中科院分区：
文献类型：
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作者：
Lebedev AA;Young P;Isupov MN;Moroz OV;Vagin AA;Murshudov GN
CCP 4模板约束库定义了用于大分子结构细化的生物聚合物、其修饰物和配体的约束。JLigand是一个图形编辑器，用于生成新配体和共价键的描述。生物大分子是聚合物，因此用于大分子精制的约束可以细分为两组：施加于全部属于同一单体的原子的约束和与单体之间的共价键相关的约束。CCP 4模板-约束库包含三种类型的定义模板约束的数据条目：单体及其修饰的描述（均用于单体内约束）和单体间约束的链接描述。该库提供了蛋白质、DNA和RNA链的修饰和连接的通用描述，以及一些翻译后修饰，包括糖基化。特定于结构的模板约束可以在用户的附加约束库中定义。在这里，JLigand，一个新的CCP 4图形界面LibCheck和REFMAC已开发管理用户的库和生成新的单体条目，以及新的链接和相关的修改条目进行了描述。
The CCP4 template-restraint library defines restraints for biopolymers, their modifications and ligands that are used in macromolecular structure refinement. JLigand is a graphical editor for generating descriptions of new ligands and covalent linkages. Biological macromolecules are polymers and therefore the restraints for macromolecular refinement can be subdivided into two sets: restraints that are applied to atoms that all belong to the same monomer and restraints that are associated with the covalent bonds between monomers. The CCP4 template-restraint library contains three types of data entries defining template restraints: descriptions of monomers and their modifications, both used for intramonomer restraints, and descriptions of links for intermonomer restraints. The library provides generic descriptions of modifications and links for protein, DNA and RNA chains, and for some post-translational modifications including glycosylation. Structure-specific template restraints can be defined in a user’s additional restraint library. Here, JLigand, a new CCP4 graphical interface to LibCheck and REFMAC that has been developed to manage the user’s library and generate new monomer entries is described, as well as new entries for links and associated modifications.