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.