CCBuilder 2.0: Powerful and accessible coiled-coil modeling.
CCBuilder 2.0: Powerful and accessible coiled-coil modeling.
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DOI：
10.1002/pro.3279
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发表时间：
2018-01
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;Woolfson DN
越来越多的用户友好和可获得的生物分子建模计算工具将扩大生物分子工程和设计的覆盖范围和应用。对于蛋白质建模来说，一个关键的挑战是将3D蛋白质折叠的复杂性降低为一组参数方程，而这些方程仍然准确地捕捉到这些结构的显著特征。目前，这对于蛋白质的一个子集，即重复蛋白质是可能的。α螺旋螺旋线圈提供了一个这样的例子，它代表了≈所有已知蛋白质编码区的3-5%。盘绕线圈是可以通过一组小的结构参数来描述的α螺旋束。在这里，我们描述了如何在一个名为CCBuilder2.0的简单易用的Web应用程序中实现这种参数描述，该应用程序用于建模和优化α螺旋螺旋和基于多脯氨酸的胶原蛋白三螺旋。它有许多应用，从提供模型来帮助X射线结晶学的分子替换，在硅胶模型的建立和天然和设计的蛋白质组件的工程中，到创建完全从头开始的“暗物质”蛋白质结构。CCBuilder 2.0是一个基于Web的应用程序，其代码是开源的，可以免费下载。Http://coiledcoils.chm.bris.ac.uk/ccbuilder2.我们已经创建了CCBuilder2.0，这是一个易于使用的基于Web的应用程序，可以对一整类蛋白质的结构进行建模，这类蛋白质是α螺旋螺旋线圈，估计占自然界所有蛋白质的3%-5%。CCBuilder 2.0将有助于大量从事蛋白质结构测定等基础研究的蛋白质科学家，以及包括设计和设计在生物技术中具有潜在应用的新型蛋白质在内的更多应用研究。
The increased availability of user‐friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely, repeat proteins. The α‐helical coiled coil provides one such example, which represents ≈ 3–5% of all known protein‐encoding regions of DNA. Coiled coils are bundles of α helices that can be described by a small set of structural parameters. Here we describe how this parametric description can be implemented in an easy‐to‐use web application, called CCBuilder 2.0, for modeling and optimizing both α‐helical coiled coils and polyproline‐based collagen triple helices. This has many applications from providing models to aid molecular replacement for X‐ray crystallography, in silico model building and engineering of natural and designed protein assemblies, and through to the creation of completely de novo “dark matter” protein structures. CCBuilder 2.0 is available as a web‐based application, the code for which is open‐source and can be downloaded freely. http://coiledcoils.chm.bris.ac.uk/ccbuilder2. We have created CCBuilder 2.0, an easy to use web‐based application that can model structures for a whole class of proteins, the α‐helical coiled coil, which is estimated to account for 3–5% of all proteins in nature. CCBuilder 2.0 will be of use to a large number of protein scientists engaged in fundamental studies, such as protein structure determination, through to more‐applied research including designing and engineering novel proteins that have potential applications in biotechnology.
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影响因子：
38.3
作者：
通讯作者：
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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：
10.1126/science.aad8036
发表时间：
2016-05-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jacobs TM;Williams B;Williams T;Xu X;Eletsky A;Federizon JF;Szyperski T;Kuhlman B
通讯作者：
Kuhlman B