Fpocket: an open source platform for ligand pocket detection.
Fpocket: an open source platform for ligand pocket detection.
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DOI：
10.1186/1471-2105-10-168
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发表时间：
2009-06-02
影响因子：
3
通讯作者：
Tuffery P
中科院分区：
文献类型：
--
作者：
Le Guilloux V;Schmidtke P;Tuffery P
虚拟筛选方法开始得到广泛认可，成为识别药物发现研究的热门产品、候选药物和先导化合物的有效方法。其中，基于结构的虚拟筛选（SBVS）方法旨在将小化合物集合对接到目标结构中，以识别有效的化合物。对于 SBVS 来说，识别蛋白质结构中的候选口袋是一个关键特征，近年来人们对开发蛋白质表面口袋和空腔检测方法的兴趣日益浓厚。 Fpocket 是一个开源口袋检测包，基于 Voronoi 曲面细分和 alpha 球体，构建在公开可用的包 Qhull 之上。模块化源代码围绕一个中央函数库进行组织，这是三个主要程序的基础：(i) Fpocket，用于执行口袋识别，(ii) Tpocket，用于组织一组已知蛋白质-配体复合物上的口袋检测基准，以及 (iii) Dpocket，用于收集一组蛋白质上的口袋描述符值。 Fpocket 是用 C 编程语言编写的，这使得它成为一个非常适合愿意开发新的评分函数并大规模提取各种口袋描述符的科学界的平台。 Fpocket 1.0依靠简单的评分功能，能够分别从holo和apo蛋白中检测到排名最好的三个口袋中94%和92%的口袋，超越了该领域的标准，同时速度更快。 Fpocket 为与蛋白质袋检测、高效袋描述符提取或成药性预测相关的进一步开发提供了快速、开源和稳定的基础。 Fpocket 可根据 GNU GPL 许可证免费获得，网址为 。
Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approaches aim at docking collections of small compounds in the target structure to identify potent compounds. For SBVS, the identification of candidate pockets in protein structures is a key feature, and the recent years have seen increasing interest in developing methods for pocket and cavity detection on protein surfaces. Fpocket is an open source pocket detection package based on Voronoi tessellation and alpha spheres built on top of the publicly available package Qhull. The modular source code is organised around a central library of functions, a basis for three main programs: (i) Fpocket, to perform pocket identification, (ii) Tpocket, to organise pocket detection benchmarking on a set of known protein-ligand complexes, and (iii) Dpocket, to collect pocket descriptor values on a set of proteins. Fpocket is written in the C programming language, which makes it a platform well suited for the scientific community willing to develop new scoring functions and extract various pocket descriptors on a large scale level. Fpocket 1.0, relying on a simple scoring function, is able to detect 94% and 92% of the pockets within the best three ranked pockets from the holo and apo proteins respectively, outperforming the standards of the field, while being faster. Fpocket provides a rapid, open source and stable basis for further developments related to protein pocket detection, efficient pocket descriptor extraction, or drugablity prediction purposes. Fpocket is freely available under the GNU GPL license at .
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作者：
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