title: Reprint of: fRMSDchiral: a novel algorithm to represent differences between positions of stereoisomers in complex with dissymmetric binding site.
abstract: The ability of molecules to distinguish between optical isomers is crucial for living systems. The change of position of one enantiomer in respect to the position of the second enantiomer within an asymmetric binding site may be analyzed on different levels. Root Mean Square Deviation (RMSD) may be used for such analyses with low precision. Additional fragment level variants of RMSD allow for more precise definition of differences in location of the main molecular features responsible for recognition of stereoisomers by a selector. Three fRMSDchiral parameters appear to be very useful to precisely quantify the change in orientations of stereoisomers. Proposed calculation emerges as interesting assistance in interpretation of consequences of formation differential interaction(s) responsible for a chiral recognition process.
authors.affiliation: Medical University of Lublin, Laboratory of Medicinal Chemistry and Neuroengineering, Lublin, Poland.
authors.forename: Rafal D
authors.initials: RD
authors.lastname: Urniaz
authors.affiliation: Medical University of Lublin, Laboratory of Medicinal Chemistry and Neuroengineering, Lublin, Poland.
authors.forename: Ewelina E
authors.initials: EE
authors.lastname: Rutkowska
authors.affiliation: Medical University of Lublin, Laboratory of Medicinal Chemistry and Neuroengineering, Lublin, Poland.
authors.forename: Anita
authors.initials: A
authors.lastname: Plazinska
authors.affiliation: Medical University of Lublin, Laboratory of Medicinal Chemistry and Neuroengineering, Lublin, Poland. Electronic address: krzysztof.jozwiak@umlub.pl.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Jozwiak
keywords: Chiral recognition; Docking; Fragment RMSD; Molecular dynamics; Molecular modeling