GEOMETRIC VERSUS TOPOLOGICAL CLUSTERING - AN INSIGHT INTO CONFORMATION MAPPING

Clustering molecular conformations into ''families'' is a common proce dure in conformational analysis of molecular systems. An implicit assu mption which often underlies this clustering approach is that the resu lting geometric families reflect the energetic structure of the system 's potential energy surface. In a broader context we address the quest ion whether structural similarity is correlated with energy basins, i. e., whether conformations that belong to the same energy basin are als o geometrically similar. 'Topological mapping' and principal coordinat e projections are used here to address this question and to assess the quality of the 'family clustering' procedure, Applying the analysis t o a small tetrapeptide it was found that the general correlation that exists between energy basins and structural similarity is not absolute . Clusters generated by the geometric 'family clustering' procedure do not always reflect the underlying energy basins. In particular it was found that the 'family tree' that is generated by the 'family cluster ing' procedure is completely inconsistent with its real topological co unterpart, the 'disconnectivity' graph of this system. It is also demo nstrated that principal coordinate analysis is a powerful visualizatio n technique which, at least for this system, works better when distanc es are measured in dihedral angle space rather than in cartesian space . (C) 1997 Wiley-Liss, Inc.