Advances in molecular-replacement procedures: the REVAN pipeline.

Benedetta Carrozzini, Giovanni Luca Cascarano, Carmelo Giacovazzo, Annamaria Mazzone
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引用次数: 7

Abstract

The REVAN pipeline aiming at the solution of protein structures via molecular replacement (MR) has been assembled. It is the successor to REVA, a pipeline that is particularly efficient when the sequence identity (SI) between the target and the model is greater than 0.30. The REVAN and REVA procedures coincide when the SI is >0.30, but differ substantially in worse conditions. To treat these cases, REVAN combines a variety of programs and algorithms (REMO09, REFMAC, DM, DSR, VLD, free lunch, Coot, Buccaneer and phenix.autobuild). The MR model, suitably rotated and positioned, is first refined by a standard REFMAC refinement procedure, and the corresponding electron density is then submitted to cycles of DM-VLD-REFMAC. The next REFMAC applications exploit the better electron densities obtained at the end of the VLD-EDM sections (a procedure called vector refinement). In order to make the model more similar to the target, the model is submitted to mutations, in which Coot plays a basic role, and it is then cyclically resubmitted to REFMAC-EDM-VLD cycles. The phases thus obtained are submitted to free lunch and allow most of the test structures studied by DiMaio et al. [(2011), Nature (London), 473, 540-543] to be solved without using energy-guided programs.

分子替代程序的进展:REVAN管道。
旨在通过分子替代(MR)解决蛋白质结构的REVAN管道已经组装完成。它是REVA的继承者,当目标和模型之间的序列同一性(SI)大于0.30时,REVA管道特别有效。当SI >0.30时,REVAN和REVA程序一致,但在较差的条件下差异很大。为了处理这些情况,REVAN结合了各种程序和算法(REMO09, REFMAC, DM, DSR, VLD, free lunch, Coot, Buccaneer和phoenix .autobuild)。首先通过标准的REFMAC改进程序对MR模型进行适当的旋转和定位,然后将相应的电子密度提交给DM-VLD-REFMAC循环。下一个REFMAC应用程序利用在VLD-EDM部分结束时获得的更好的电子密度(称为矢量细化的过程)。为了使模型更接近靶标,将模型提交给突变,其中Coot起基本作用,然后将其循环地重新提交给REFMAC-EDM-VLD循环。这样得到的相位是免费的,并且允许DiMaio等人[(2011),Nature (London), 473, 540-543]研究的大多数测试结构无需使用能量引导程序即可求解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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