Reverse engineering chemical structures from molecular descriptors: how many solutions?

J Comput Aided Mol Des. 2005 Sep-Oct;19(9-10):637-50. doi: 10.1007/s10822-005-9007-1. Epub 2005 Nov 3.


Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chemical Engineering
  • Computer Simulation*
  • Databases, Factual
  • Drug Design
  • Drug Industry
  • Models, Chemical*
  • Molecular Structure
  • Quantitative Structure-Activity Relationship
  • Stochastic Processes