从简化表示重建全原子蛋白质模型的快速方法。
Fast procedure for reconstruction of full-atom protein models from reduced representations.
作者信息
Rotkiewicz Piotr, Skolnick Jeffrey
机构信息
Burnham Institute for Medical Research, 10901 N. Torrey Pines Road, La Jolla, California 92037, USA.
出版信息
J Comput Chem. 2008 Jul 15;29(9):1460-5. doi: 10.1002/jcc.20906.
Abstract
We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly suitable as an intermediate step between coarse-grained model-based structure prediction and applications requiring an all-atom structure, such as molecular dynamics, protein-ligand docking, structure-based function prediction, or assessment of quality of the predicted structure. The accuracy of the method was tested on a set of high-resolution crystallographic structures as well as on a set of low-resolution protein decoys generated by a protein structure prediction algorithm TASSER. The method is implemented as a standalone program that is available for download from http://cssb.biology.gatech.edu/skolnick/files/PULCHRA.
摘要
我们介绍了PULCHRA，这是一种从简化的蛋白质表示开始重建全原子蛋白质模型的快速且稳健的方法。该算法特别适合作为基于粗粒度模型的结构预测与需要全原子结构的应用（如分子动力学、蛋白质-配体对接、基于结构的功能预测或预测结构质量评估）之间的中间步骤。该方法的准确性在一组高分辨率晶体结构以及由蛋白质结构预测算法TASSER生成的一组低分辨率蛋白质诱饵上进行了测试。该方法作为一个独立程序实现，可从http://cssb.biology.gatech.edu/skolnick/files/PULCHRA下载。
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