Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates
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DOI：
10.1002/jcc.20624
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发表时间：
2007-07-15
影响因子：
3
通讯作者：
Kolinski, Andrzej
中科院分区：
文献类型：
--
作者：
Gront, Dominik;Kmiecik, Sebastian;Kolinski, Andrzej
在这一贡献中，我们提出了一种具有很高计算效率和高精度的蛋白质骨架重建算法。从α碳轨迹重建主链原子坐标是蛋白质建模中的一项常见任务，包括从头结构预测、比较建模和实验数据处理。这项工作所采用的方法遵循了一些早期解决问题的方法的主要思想。本方法的细节和精心设计是新的，并导致该算法的性能优于所有常用的早期应用程序。BBQ程序已经在天然结构和近天然诱饵模型上进行了广泛的测试，并与现有的不同方法进行了比较。获得的结果提供了现有工具的综合基准，并评估了它们在使用蛋白质构象空间的简化表示法进行大规模建模时的适用性。烧烤套装可从我们的网站http://biocomp.chem.uw.edu.pl/services/BBQ/.下载该网页还提供了详细介绍BBQ功能的用户手册。(C)2007年威利期刊公司。
In this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Reconstruction of the main chain atomic coordinates from the alpha carbon trace is a common task in protein modeling, including de novo structure prediction, comparative modeling, and processing experimental data. The method employed in this work follows the main idea of some earlier approaches to the problem. The details and careful design of the present approach are new and lead to the algorithm that outperforms all commonly used earlier applications. BBQ (Backbone Building from Quadrilaterals) program has been extensively tested both on native structures as well as on near-native decoy models and compared with the different available existing methods. Obtained results provide a comprehensive benchmark of existing tools and evaluate their applicability to a large scale modeling using a reduced representation of protein conformational space. The BBQ package is available for downloading from our website at http://biocomp.chem.uw.edu.pl/services/BBQ/. This webpage also provides a user manual that describes BBQ functions in detail. (C) 2007 Wiley Periodicals, Inc.