Assessment of automatic ligand building in ARP/wARP
Assessment of automatic ligand building in ARP/wARP
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DOI：
10.1107/s0907444906023389
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发表时间：
2007-01-01
期刊：
影响因子：
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通讯作者：
Lamzin, Victor S.
中科院分区：
文献类型：
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作者：
Evrard, Guillaume X.;Langer, Gerrit G.;Lamzin, Victor S.
ARP/wARP 6.1版本的配体构建模块的效率已经通过对来自PDB的各种蛋白质配体复合物的广泛测试进行了评估，这些测试可从乌普萨拉电子密度服务器获得。ARP/wARP中的配体构建主要包括两个步骤：自动识别配体的位置和实际构建配体的原子模型。第一步对于大配体来说是最成功的。第二步，配体构建，更强大的是高分辨率的x射线数据和中小尺寸的配体。这两个步骤对于具有低到中等原子位移参数的配体是成功的。这些结果突出了配体构建方法和大规模验证程序的优缺点，并有助于确定进一步改进的方法。
The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein-ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement.