REFMAC5 dictionary:: organization of prior chemical knowledge and guidelines for its use
REFMAC5 dictionary:: organization of prior chemical knowledge and guidelines for its use
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DOI：
10.1107/s0907444904023510
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发表时间：
2004-12-01
影响因子：
2.2
通讯作者：
Murshudov, GN
中科院分区：
文献类型：
--
作者：
Vagin, AA;Steiner, RA;Murshudov, GN
大分子结构优化的最重要方面之一是使用先前的化学知识。键长、键角和其他化学性质在约束细化中用作辅助条件。这一贡献描述了组织和某些方面的使用灵活的和人类/机器可读的字典的化学知识使用的最大似然大分子细化程序REFMAC 5。该词典存储了有关单体的信息，这些单体代表生物大分子（氨基酸，核酸和DNA）的组成结构单元，以及在大分子晶体学中常见的许多有机/无机化合物。它还描述了结构单元由于化学反应和聚合物形成所需的连接而进行的修饰。目前可提供2000多个单体条目、100个修改条目和200个链接条目。更新和增加新的条目到字典的算法和工具也已经开发出来，并在这里介绍。在许多情况下，REFMAC 5字典允许在REFMAC 5细化运行中完全自动生成约束。
One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine-readable dictionary of prior chemical knowledge used by the maximum-likelihood macromolecular-refinement program REFMAC5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules ( amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.