Carrozzini Benedetta, Cascarano Giovanni Luca, Giacovazzo Carmelo, Mazzone Annamaria
Istituto di Cristallografia, CNR, Via G. Amendola 122/o, 70126 Bari, Italy.
Acta Crystallogr D Biol Crystallogr. 2015 Sep;71(Pt 9):1856-63. doi: 10.1107/S1399004715012730. Epub 2015 Aug 28.
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.
旨在通过分子置换（MR）解决蛋白质结构问题的REVAN管道已经组装完成。它是REVA的后继版本，当目标与模型之间的序列同一性（SI）大于0.30时，REVA管道特别高效。当SI>0.30时，REVAN和REVA程序一致，但在更差的条件下有很大差异。为了处理这些情况，REVAN结合了多种程序和算法（REMO09、REFMAC、DM、DSR、VLD、免费午餐、Coot、Buccaneer和phenix.autobuild）。经过适当旋转和定位的MR模型首先通过标准的REFMAC精修程序进行精修，然后将相应的电子密度提交给DM-VLD-REFMAC循环。接下来的REFMAC应用利用在VLD-EDM部分结束时获得的更好的电子密度（一种称为向量精修的程序）。为了使模型更类似于目标，模型会进行突变，其中Coot起着基本作用，然后将其循环提交给REFMAC-EDM-VLD循环。由此获得的相位会提交给免费午餐，并且可以在不使用能量引导程序的情况下解决DiMaio等人[（2011年），《自然》（伦敦），473，540 - 543]研究的大多数测试结构。
