title: Protein binding site analysis by means of structural interaction fingerprint patterns.
abstract: We introduce a new approach to the known concept of interaction profiles, based on Structural Interaction Fingerprints (SIFt), for precise and rapid binding site description. A set of scripts for batch generation and analysis of SIFt were prepared, and the implementation is computationally efficient and supports parallelization. It is based on a 9-digit binary interaction pattern that describes physical ligand-protein interactions in structures and models of ligand-protein complexes. The tool performs analysis and identifies binding site residues (crucial and auxiliary) and classifies interactions according to type (hydrophobic, aromatic, charge, polar, side chain, and backbone). It is convenient and easy to use, and gives manageable output data for both, interpretation and further processing. In the presented Letter, SIFts are applied to analyze binding sites in models of antagonist-5-HT7 receptor complexes and structures of cyclin dependent kinase 2-ligand complexes.
authors.affiliation: Department of Medicinal Chemistry, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343 Krakow, Poland.
authors.forename: Stefan
authors.initials: S
authors.lastname: Mordalski
authors.forename: Tomasz
authors.initials: T
authors.lastname: Kosciolek
authors.forename: Kurt
authors.initials: K
authors.lastname: Kristiansen
authors.forename: Ingebrigt
authors.initials: I
authors.lastname: Sylte
authors.forename: Andrzej J
authors.initials: AJ
authors.lastname: Bojarski
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D051357:Cyclin-Dependent Kinase 2 / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods; D011485:Protein Binding; D011985:Receptors, Serotonin / Q000737:chemistry* / Q000378:metabolism*; D012702:Serotonin Antagonists / Q000494:pharmacology*
chemical_list: D008024:Ligands; D011985:Receptors, Serotonin; D012702:Serotonin Antagonists; C104425:serotonin 7 receptor; D051357:Cyclin-Dependent Kinase 2