CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies.
CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies.
复制标题
DOI：
10.1093/bioinformatics/btu502
复制
发表时间：
2014-11-01
期刊：
影响因子：
--
通讯作者：
Woolfson DN
中科院分区：
文献类型：
--
作者：
Wood CW;Bruning M;Ibarra AÁ;Bartlett GJ;Thomson AR;Sessions RB;Brady RL;Woolfson DN
动机：在原子水平上精确建模蛋白质结构的能力支撑着理解蛋白质折叠、可预测地工程化天然蛋白质和从头设计蛋白质的努力。基于同源性的方法已经建立并产生了令人印象深刻的结果。然而，这些仅限于天然蛋白质呈现和解析的结构。更广泛地解决这个问题并获得真正的从头算模型需要对蛋白质折叠进行数学描述;用天然，工程或从头序列装饰这些折叠的方法;以及对所得模型进行评分的方法。结果如下：我们提出了CCBuilder，一个基于网络的应用程序，解决了一个定义的，但大类蛋白质结构，α-螺旋卷曲螺旋的问题。CCBuilder生成卷曲螺旋骨架，在这些框架上构建侧链，并提供一系列指标来衡量模型的质量。其简单的图形用户界面提供了广泛的功能，允许用户构建和评估模型，其中螺旋几何形状，卷曲螺旋结构和拓扑结构以及蛋白质序列可以快速变化。我们通过组装PDB中653个卷曲螺旋结构的模型来展示CCBuilder的实用性，这些模型覆盖了已知卷曲螺旋类型的96%以上，并通过生成罕见和新生卷曲螺旋结构的模型来展示CCBuilder的实用性。可用性和实施：CCBuilder免费提供，无需注册，网址：http://coiledcoils.chm.bris.ac.uk/app/cc_builder/联系人：D.N. bristol.ac.uk或Chris. bristol.ac.uk
Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo. Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures. Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder/ Contact: D.N.Woolfson@bristol.ac.uk or Chris.Wood@bristol.ac.uk
登录
查看更多内容
影响因子：
5.6
作者：
Grigoryan G;Degrado WF
通讯作者：
Degrado WF
影响因子：
2.9
作者：
Krivov, Georgii G.;Shapovalov, Maxim V.;Dunbrack, Roland L., Jr.
通讯作者：
Dunbrack, Roland L., Jr.
影响因子：
5.8
作者：
Delorenzi, M;Speed, T
通讯作者：
Speed, T
DOI：
10.1080/07391102.2000.10506570
发表时间：
2000-04-01
影响因子：
4.4
作者：
Bansal, M;Kumar, S;Velavan, R
通讯作者：
Velavan, R
影响因子：
56.9
作者：
HARBURY, PB;ZHANG, T;ALBER, T
通讯作者：
ALBER, T