title: Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces.
abstract: 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.
authors.affiliation: Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany.
authors.forename: Therese
authors.initials: T
authors.lastname: Inhester
authors.affiliation: Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bietz
authors.affiliation: Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Hilbig
authors.affiliation: Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany.
authors.forename: Robert
authors.initials: R
authors.lastname: Schmidt
authors.affiliation: Center for Bioinformatics, University of Hamburg , Bundesstrasse 43, 20146 Hamburg, Germany.
authors.forename: Matthias
authors.identifier: 0000-0002-9553-6531
authors.initials: M
authors.lastname: Rarey
mesh_terms: D000465:Algorithms; D057225:Data Mining / Q000379:methods*; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D013997:Time Factors
chemical_list: D008024:Ligands; D011506:Proteins