P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure.
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure.
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DOI：
10.1186/s13321-018-0285-8
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发表时间：
2018-08-14
影响因子：
8.6
通讯作者：
Hoksza D
中科院分区：
文献类型：
--
作者：
Krivák R;Hoksza D
从蛋白质结构预测配体结合位点在蛋白质功能的阐明和基于结构的药物发现方面具有许多应用。它通常只是复杂的计算药物设计工作中的一个步骤。尽管迄今为止已经发布了许多方法，但其中只有少数适合在自动管道中使用或处理大型数据集。 这些用例需要稳定性和速度，这使得许多最近推出的基于模板或仅作为Web服务器提供的工具不合格。我们提出了P2 Rank，一个独立的无模板工具，用于基于机器学习预测配体结合位点。它是基于对局部化学邻域的配位能力的预测，这些化学邻域集中在蛋白质的溶剂可及表面上的点上。 我们发现P2 Rank优于几个现有的工具，其中包括两个广泛使用的独立工具（Fpocket，SiteHound），一个全面的基于共识的工具（MetaPocket 2.0），以及最近的基于深度学习的方法（DeepSite）。P2 Rank属于最快的可用工具（对一种蛋白质的预测需要不到1秒），具有多线程实现的额外优势。P2 Rank是一个新的开源软件包，用于从蛋白质结构预测配体结合位点。它是一个用户友好的独立命令行程序和Java库。P2 Rank具有轻量级安装，不依赖于其他生物信息学工具或大型结构或序列数据库。由于其速度和进行全自动预测的能力，它特别适合处理大型数据集或作为可扩展的结构生物信息学管道的组成部分。本文的在线版本（10.1186/s13321-018-0285-8）包含补充材料，可供授权用户使用。
Ligand binding site prediction from protein structure has many applications related to elucidation of protein function and structure based drug discovery. It often represents only one step of many in complex computational drug design efforts. Although many methods have been published to date, only few of them are suitable for use in automated pipelines or for processing large datasets. These use cases require stability and speed, which disqualifies many of the recently introduced tools that are either template based or available only as web servers. We present P2Rank, a stand-alone template-free tool for prediction of ligand binding sites based on machine learning. It is based on prediction of ligandability of local chemical neighbourhoods that are centered on points placed on the solvent accessible surface of a protein. We show that P2Rank outperforms several existing tools, which include two widely used stand-alone tools (Fpocket, SiteHound), a comprehensive consensus based tool (MetaPocket 2.0), and a recent deep learning based method (DeepSite). P2Rank belongs to the fastest available tools (requires under 1 s for prediction on one protein), with additional advantage of multi-threaded implementation. P2Rank is a new open source software package for ligand binding site prediction from protein structure. It is available as a user-friendly stand-alone command line program and a Java library. P2Rank has a lightweight installation and does not depend on other bioinformatics tools or large structural or sequence databases. Thanks to its speed and ability to make fully automated predictions, it is particularly well suited for processing large datasets or as a component of scalable structural bioinformatics pipelines. The online version of this article (10.1186/s13321-018-0285-8) contains supplementary material, which is available to authorized users.
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影响因子：
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作者：
Ghersi, Dario;Sanchez, Roberto
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作者：
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作者：
Halgren, Thomas A.
通讯作者：
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作者：
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通讯作者：
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影响因子：
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作者：
Gao J;Zhang Q;Liu M;Zhu L;Wu D;Cao Z;Zhu R
通讯作者：
Zhu R