Department of Sciences, University of Roma Tre, 00146 Rome, Italy, Department of Science and Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam and.
Department of Sciences, University of Roma Tre, 00146 Rome, Italy.
Bioinformatics. 2015 Dec 15;31(24):4020-2. doi: 10.1093/bioinformatics/btv489. Epub 2015 Aug 26.
In recent years, structural genomics and ab initio molecular modeling activities are leading to the availability of a large number of structural models of proteins whose biochemical function is not known. The aim of this study was the development of a novel software tool that, given a protein's structural model, predicts the presence and identity of active sites and/or ligand binding sites.
The algorithm implemented by ligand binding site recognition application (LIBRA) is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. The algorithm makes use of two predefined databases for active sites and ligand binding sites, respectively, derived from the Catalytic Site Atlas and the Protein Data Bank. Tests indicate that LIBRA is able to identify the correct binding/active site in 90% of the cases analyzed, 90% of which feature the identified site as ranking first. As far as ligand binding site recognition is concerned, LIBRA outperforms other structure-based ligand binding sites detection tools with which it has been compared.
The application, developed in Java SE 7 with a Swing GUI embedding a JMol applet, can be run on any OS equipped with a suitable Java Virtual Machine (JVM), and is available at the following URL: http://www.computationalbiology.it/software/LIBRAv1.zip.
近年来，结构基因组学和从头分子建模活动的发展使得大量未知生化功能的蛋白质结构模型得以实现。本研究的目的是开发一种新的软件工具，该工具可以预测蛋白质结构模型中活性位点和/或配体结合位点的存在和身份。
配体结合位点识别应用程序（LIBRA）中实现的算法基于图论方法，用于在输入蛋白质和一组已知功能位点之间找到相似残基的最大子集。该算法分别使用两个预定义的数据库，分别来自 Catalytic Site Atlas 和 Protein Data Bank，用于活性位点和配体结合位点。测试表明，LIBRA 能够在分析的 90%的案例中识别正确的结合/活性位点，其中 90%的案例中识别出的位点排名第一。就配体结合位点识别而言，LIBRA 优于其他基于结构的配体结合位点检测工具，已经与这些工具进行了比较。
该应用程序是使用 Java SE 7 开发的，具有 Swing GUI 嵌入 JMol 小程序，可以在任何配备合适 Java 虚拟机 (JVM) 的操作系统上运行，并可在以下网址获得：http://www.computationalbiology.it/software/LIBRAv1.zip。
