Stierand Katrin, Maass Patrick C, Rarey Matthias
Center for Bioinformatics (ZBH), University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.
Bioinformatics. 2006 Jul 15;22(14):1710-6. doi: 10.1093/bioinformatics/btl150. Epub 2006 Apr 21.
In this paper a new algorithmic approach is presented, which automatically generates structure diagrams of molecular complexes. A complex diagram contains the ligand, the amino acids of the protein interacting with the ligand and the hydrophilic interactions schematized as dashed lines between the corresponding atoms. The algorithm is based on a combinatorial optimization strategy which solves parts of the layout problem non-heuristically. The depicted molecules are represented as structure diagrams according to the chemical nomenclature. Due to the frequent usage of complex diagrams in the scientific literature as well as in text books dealing with structural biology, biochemistry and medicinal chemistry, the new algorithm is a key element for computer applications in these areas.
The method was implemented in the new software tool PoseView. It was tested on a representative dataset containing 305 protein-ligand complexes in total from the Brookhaven Protein Data Bank. PoseView was able to find collision-free layouts for more than three quarters of all complexes. In the following the layout generation algorithm is presented and, additional to the statistical results, representative test cases demonstrating the challenges of the layout generation will be discussed.
The method is available as a webservice at http://www.zbh.uni-hamburg.de/poseview.
本文提出了一种新的算法方法，可自动生成分子复合物的结构图。复合物图包含配体、与配体相互作用的蛋白质氨基酸以及以相应原子之间的虚线示意的亲水相互作用。该算法基于一种组合优化策略，可非启发式地解决部分布局问题。所描绘的分子根据化学命名法表示为结构图。由于复合物图在科学文献以及涉及结构生物学、生物化学和药物化学的教科书中经常使用，因此新算法是这些领域计算机应用的关键要素。
该方法在新软件工具PoseView中得以实现。它在一个代表性数据集上进行了测试，该数据集总共包含来自布鲁克海文蛋白质数据库的305个蛋白质 - 配体复合物。PoseView能够为超过四分之三的复合物找到无碰撞布局。接下来将介绍布局生成算法，除统计结果外，还将讨论展示布局生成挑战的代表性测试案例。
该方法可作为网络服务在http://www.zbh.uni-hamburg.de/poseview获取。
