Index-Based Searching of Interaction Patterns in Large Collections of Protein–Ligand Interfaces

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