Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures

PozharskiE.; WeichenbergerC.X.; RuppB.

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Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures

机译：配体的技术、工具和最佳实践从他们的电子密度分析和结果应用沉积晶体结构

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As a result of substantial instrumental automation and the continuing improvement of software, crystallographic studies of biomolecules are conducted by non-experts in increasing numbers. While improved validation almost ensures that major mistakes in the protein part of structure models are exceedingly rare, in ligand-protein complex structures, which in general are most interesting to the scientist, ambiguous ligand electron density is often difficult to interpret and the modelled ligands are generally more difficult to properly validate. Here, (i) the primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) the most common categories of building errors or overinterpretation are classified; (iii) a few instructive and specific examples are discussed in detail, including an electron-density-based analysis of ligand structures that do not contain any ligands; (iv) means of avoiding such mistakes are suggested and the implications for database validity are discussed and (v) a user-friendly software tool that allows non-expert users to conveniently inspect ligand density is provided.

机译：由于大量的仪器自动化和持续改进的软件,晶体的研究生物分子由非专家的数量与日俱增。虽然几乎可以确保改进的验证重大错误的蛋白质结构的一部分在ligand-protein模型是极其罕见的一般来说是最复杂的结构有趣的科学家,模棱两可的配体电子密度往往是难以解释和模仿配体通常是更多很难正确地验证。主要技术原因和潜在的人类因素导致配体结构中存在的问题提出了模型;类别的建筑或错误overinterpretation进行分类;有益的和具体的例子进行了讨论在细节,包括一个electron-density-based不含配体结构的分析任何配体;建议和对数据库的影响是什么效度是一个用户友好的讨论和(v)允许非专业用户的软件工具方便检查配体密度。

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《Acta crystallographica. Section D, Biological crystallography.》 |2013年第2期|150-167|共18页
作者
PozharskiE.; WeichenbergerC.X.; RuppB.;
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作者单位

Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, I-39100 Bozen;

K.-k. Hofkristallamt, 991 Audrey Place, Vista CA 92084, United States;

Department of Pharmaceutical Sciences, University of Maryland, Baltimore MD, United States;

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正文语种英语
中图分类化学;
关键词
density determination; Human factors; crystal structureElectron densityBest Practicescomplex structureBiomolecules;

机译：密度测定,人为因素;晶体structureElectron densityBest PracticescomplexstructureBiomolecules;

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Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures

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