Practically useful: what the Rosetta protein modeling suite can do for you.
Practically useful: what the Rosetta protein modeling suite can do for you.
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DOI：
10.1021/bi902153g
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发表时间：
2010-04-13
期刊：
影响因子：
2.9
通讯作者：
Meiler, Jens
中科院分区：
文献类型：
--
作者：
Kaufmann, Kristian W.;Lemmon, Gordon H.;DeLuca, Samuel L.;Sheehan, Jonathan H.;Meiler, Jens
这篇综述的目的是使研究人员能够使用Rosetta软件包进行生物化学和生物医学研究。我们简要回顾了Rosetta解决的六个最常见的研究问题。对于这六个任务中的每一个，我们都提供了一个教程来说明基本的Rosetta协议。Rosetta方法最初是为从头蛋白质结构预测而开发的，并且经常是两年一度的社区结构预测关键评估中表现最好的方法之一。对于少于125个氨基酸的蛋白质结构域的预测通常具有优于5.0 μ m的骨架均方根偏差。更令人印象深刻的是，有几种情况下，罗塞塔已被用于预测结构，原子级精度优于2.5 μ m。除了从头结构预测，Rosetta还具有分子对接，同源建模，从稀疏实验NMR或EPR数据确定蛋白质结构和蛋白质设计的方法。Rosetta已被用于精确设计新的蛋白质结构，预测蛋白质-蛋白质复合物的结构，设计改变特异性的蛋白质-蛋白质和蛋白质-DNA相互作用，以及稳定蛋白质和蛋白质复合物。最近，Rosetta被用于解决X射线晶体学相位问题。
The objective of this review is to enable researchers to use the software package Rosetta for biochemical and biomedicinal studies. We provide a brief review of the six most frequent research problems tackled with Rosetta. For each of these six tasks, we provide a tutorial that illustrates a basic Rosetta protocol. The Rosetta method was originally developed for de novo protein structure prediction and is regularly one of the best performers in the community-wide biennial Critical Assessment of Structure Prediction. Predictions for protein domains with fewer than 125 amino acids regularly have a backbone root-mean-square deviation of better than 5.0 Å. More impressively, there are several cases in which Rosetta has been used to predict structures with atomic level accuracy better than 2.5 Å. In addition to de novo structure prediction, Rosetta also has methods for molecular docking, homology modeling, determining protein structures from sparse experimental NMR or EPR data, and protein design. Rosetta has been used to accurately design a novel protein structure, predict the structure of protein−protein complexes, design altered specificity protein−protein and protein−DNA interactions, and stabilize proteins and protein complexes. Most recently, Rosetta has been used to solve the X-ray crystallographic phase problem.
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DOI：
10.1107/s0907444908020039
发表时间：
2009-02
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Das, Rhiju;Baker, David
通讯作者：
Baker, David
影响因子：
2.9
作者：
Das, Rhiju;Bin Qian;Baker, David
通讯作者：
Baker, David
影响因子：
2.9
作者：
Chaudhury, Sidhartha;Sircar, Aroop;Gray, Jeffrey J.
通讯作者：
Gray, Jeffrey J.
影响因子：
64.5
作者：
Burguete, Alondra Schweizer;Fenn, Timothy D.;Pfeffer, Suzanne R.
通讯作者：
Pfeffer, Suzanne R.
影响因子：
5.6
作者：
Chaudhury, Sidhartha;Gray, Jeffrey J.
通讯作者：
Gray, Jeffrey J.