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首页> 外文期刊>Acta crystallographica.Section D. Biological crystallography >PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.
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PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.

机译：PRODRG:高通量结晶学的工具protein-ligand复合物。

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摘要

The small-molecule topology generator PRODRG is described, which takes input from existing coordinates or various two-dimensional formats and automatically generates coordinates and molecular topologies suitable for X-ray refinement of protein-ligand complexes. Test results are described for automatic generation of topologies followed by energy minimization for a subset of compounds from the Cambridge Structural Database, which shows that, within the limits of the empirical GROMOS87 force field used, structures with good geometries are generated. X-ray refinement in X-PLOR/CNS, REFMAC and SHELX using PRODRG-generated topologies produces results comparable to refinement with topologies from the standard libraries. However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors.
机译：小分子拓扑生成器PRODRG从现有的描述,需要输入坐标或各种二维格式,并自动生成坐标和分子拓扑适合x射线细化protein-ligand复合物。结果描述自动生成拓扑能源最小化紧随其后从剑桥结构化合物的子集数据库,数据库显示,的限制范围内使用实证GROMOS87力场,结构具有良好的几何图形生成。x射线细化X-PLOR / CNS REFMAC SHELX使用PRODRG-generated拓扑产生结果可比性与拓扑优化从标准库。扭曲的坐标显示PRODRG开始在拓扑执行得更好配位几何和晶体的R的因素。

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