Stierand Katrin, Rarey Matthias
Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.
ChemMedChem. 2007 Jun;2(6):853-60. doi: 10.1002/cmdc.200700010.
As a result of the increasing application of structure-based drug design, the visualization of protein-ligand complexes has become an important feature in medicinal chemistry. The large number of experimentally resolved complex structures and the further development of computer-aided methods like docking or de novo design establishes new possibilities in this field. During lead finding and optimization, a manual investigation of many complexes and their interaction patterns is typically performed. We present an algorithm that automatically generates 2D-protein-ligand diagrams as a possible solution for a transparent visualization of the contact partners in a complex and as a support for scientists in the evaluation of structure-based design results. Running the software on representative test data sets, it generates collision free layouts for approximately 76% of the cases in the range of tenths of a second per complex. The success rate for complexes with ligands which have a molecular weight <500 Da is 87%.
由于基于结构的药物设计应用日益广泛，蛋白质-配体复合物的可视化已成为药物化学中的一个重要特征。大量通过实验解析的复合物结构以及对接或从头设计等计算机辅助方法的进一步发展，为该领域带来了新的可能性。在先导化合物发现和优化过程中，通常会对许多复合物及其相互作用模式进行人工研究。我们提出了一种算法，该算法可自动生成二维蛋白质-配体图，作为一种可能的解决方案，用于清晰可视化复合物中的接触伙伴，并为科学家评估基于结构的设计结果提供支持。在代表性测试数据集上运行该软件，它能在十分之几秒的时间内为大约76%的复合物生成无碰撞布局。对于分子量<500 Da的配体复合物，成功率为87%。
