Inhester Therese, Bietz Stefan, Hilbig Matthias, Schmidt Robert, Rarey Matthias
Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany.
J Chem Inf Model. 2017 Feb 27;57(2):148-158. doi: 10.1021/acs.jcim.6b00561. Epub 2017 Jan 27.
Comparison of three-dimensional interaction patterns in large collections of protein-ligand interfaces is a key element for understanding protein-ligand interactions and supports various steps in the structure-based drug design process. Different methods exist that provide query systems to search for geometrical patterns in protein-ligand complexes. However, these tools do not meet all of the requirements, which are high query variability, an adjustable search set, and high retrieval speed. Here we present a new tool named PELIKAN that is able to search for a variety of geometrical queries in large protein structure collections in a reasonably short time. The data are stored in an SQLite database that can easily be constructed from any set of protein-ligand complexes. We present different test queries demonstrating the performance of the PELIKAN approach. Furthermore, two application scenarios show the usefulness of PELIKAN in structure-based design endeavors.
在大量蛋白质-配体界面中比较三维相互作用模式，是理解蛋白质-配体相互作用的关键要素，并支持基于结构的药物设计过程中的各个步骤。存在不同的方法来提供查询系统，以搜索蛋白质-配体复合物中的几何模式。然而，这些工具并不能满足所有要求，即高查询变异性、可调整的搜索集和高检索速度。在此，我们展示了一种名为PELIKAN的新工具，它能够在合理的短时间内，在大型蛋白质结构集合中搜索各种几何查询。数据存储在一个SQLite数据库中，该数据库可以轻松地从任何一组蛋白质-配体复合物构建而成。我们展示了不同的测试查询，证明了PELIKAN方法的性能。此外，两个应用场景展示了PELIKAN在基于结构的设计工作中的有用性。
