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首页> 外文期刊>Acta crystallographica.Section D. Biological crystallography >MUMBO: a protein-design approach to crystallographic model building and refinement.
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MUMBO: a protein-design approach to crystallographic model building and refinement.

机译：马姆博:蛋白质设计的方法晶体模型的建立和细化。

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摘要

In recent years, significant progress has been achieved in automation of the crystal structure-determination process. However, the final part of this process, namely the refinement of the atomic model, is still tedious for biological macromolecules because, especially at lower resolution, it requires extensive manual intervention. Here, it is shown that computer algorithms widely used in protein-design approaches can substantially simplify this process, helping to identify the correct orientation of the side chains during refinement. This approach was implemented into the computer program MUMBO. As in many protein-design programs, side-chain rotamer diversity is generated using rotamer libraries. The selection of the best combination of side-chain orientations is based on either the dead-end elimination (DEE) theorem or a Metropolis Monte Carlo approach and on a detailed atomic scoring function that describes the molecular interactions between the rotamers. We show that this scoring function can be easily extended and complemented through the introduction of an X-ray pseudo-energy calculated from the electron density present at the position of the rotamer. This extension is fully compatible with present protein-design algorithms and it is shown for a number of test cases that using this approach model refinement is simplified and convergence occurs faster.
机译：近年来,重大的进展实现自动化的晶体结构测定的过程。这个过程的最后一部分,即细分原子模型,仍然是乏味的生物大分子,因为,特别是在低分辨率,它需要大量的手工干预。算法广泛应用于蛋白质设计方法可以大大简化过程,帮助识别正确的在细化方向的侧链。这种方法被实施到电脑马姆博。项目,侧链旋转异构体的多样性使用旋转异构体生成库。侧链的最好的组合方向是基于终端消除(迪)定理或大都市蒙特卡罗方法和详细的原子得分函数,它描述了分子旋转异构体之间的相互作用。这个得分函数可以很容易地扩展通过引入x射线补充伪能计算的电子密度出席旋转异构体的位置。这个扩展是完全兼容它显示的是蛋白质设计算法使用这种方法的测试用例数量模型细化是简化和收敛发生得更快。

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