fRMSDchiral: A novel algorithm to represent differences between positions of stereoisomers in complex with dissymmetric binding site

•Novel approaches allow explanation of chiral recognition at the molecular level.•Molecular models of diastereoisomeric complexes may be analyzed using RMSD.•Fragment RMSD allows more precise definition of differences in poses of diastereoisomers.

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.