LAFIRE: software for automating the refinement process of protein-structure analysis.
LAFIRE: software for automating the refinement process of protein-structure analysis.
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DOI：
10.1107/s0907444905038965
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发表时间：
2006-02
期刊：
影响因子：
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通讯作者：
M. Yao;Yong Zhou;I. Tanaka
中科院分区：
文献类型：
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作者：
M. Yao;Yong Zhou;I. Tanaka
在蛋白质晶体结构的多轮精修中通常需要人工干预，包括连接和/或延伸初始模型的片段，以及使用计算机图形软件重建（拟合）不匹配的残基。这种手工修改既耗时又需要大量的晶体学专业知识。因此，精化过程成为高通量结构分析的瓶颈。一个程序，局部相关系数为基础的自动拟合精化（LAFIRE），已被开发出来，以实现人工干预的自由细化。该程序旨在使用精制程序CNS1.1（CNS v.1.1）或REFMAC 5自动执行蛋白质结构精制的整个过程。自动过程从初始模型开始，该初始模型可以是近似的、片段的或甚至仅主链的，并且将其细化为包括水分子的最终模型，通过监测R（自由）因子来控制。现在已经有30多个结构使用LAFIRE在几个小时或几天内以全自动或半自动的方式成功地进行了优化。
Manual intervention is usually required in the multiple rounds of refinement of protein crystal structures, including linking and/or extending the fragments of the initial model and rebuilding (fitting) ill-matched residues using computer-graphics software. Such manual modification is both time-consuming and requires a great deal of expertise in crystallography. Consequently, the refinement process becomes the bottleneck for high-throughput structure analysis. A program, Local correlation coefficient-based Automatic FItting for REfinement (LAFIRE), has been developed to achieve manual intervention-free refinement. This program was designed to perform the entire process of protein structural refinement automatically using the refinement programs CNS1.1 (CNS v.1.1) or REFMAC5. The automatic process begins from an initial model, which can be approximate, fragmentary or even only main-chain, and refines it to the final model including water molecules, controlled by monitoring the R(free) factor. More than 30 structures have now been refined successfully in a fully or semi-automatic manner within a few hours or days using LAFIRE.