title: A topological similarity measure for proteins.
abstract: We introduce a new measure for assessing similarity among chemical structures, based on well-established computational-topology algorithms. We argue that although the method considers geometry, it is more than a mere geometric similarity measure, as it takes into account, on different geometric scales, the important topological features of the compared structures. We prove that our measure is rigorous and complies with the proper mathematical requirements. We validate the method through comparing different configurations of simple zinc finger proteins and present an application on ligands binding to membrane-proteINS extracted from the Directory of Useful Decoys: Enhanced database and corresponding decoys. This article is part of a Special Issue entitled: Viral membrane proteins - Channels for cellular networking.
authors.affiliation: Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, Heidelberg, Germany.
authors.forename: Gabriell
authors.initials: G
authors.lastname: Máté
authors.affiliation: Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, Heidelberg, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Hofmann
authors.affiliation: Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, Heidelberg, Germany.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Wenzel
authors.affiliation: Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, Heidelberg, Germany; The Jackson Laboratory, Bar Harbor, ME, USA; Shanghai Institute of Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, PR China. Electronic address: heermann@tphys.uni-heidelberg.de.
authors.forename: Dieter W
authors.initials: DW
authors.lastname: Heermann
mesh_terms: D000465:Algorithms; D011506:Proteins / Q000737:chemistry*; D016335:Zinc Fingers
chemical_list: D011506:Proteins
keywords: Jaccard index; Persistent intervals; Protein flexibility; Protein similarity; Protein structure; Similarity measure