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  • Oral presentation
  • Open Access

Structure-activity relationship analysis on the basis of matched molecular pairs

Journal of Cheminformatics20146 (Suppl 1) :O14

  • Published:


  • Core Structure
  • Lead Optimization
  • Reference Framework
  • Molecular Pair
  • Molecular Core

Matched molecular pairs (MMPs), i.e., pairs of compounds that are related to each other by a specific molecular transformation, have become an integral tool of drug discovery [1, 2]. Generally spoken, matched molecular pair analysis (MMPA) aims at the extraction of all MMPs from a set of compounds and their association with calculated or measured property changes. Using public bioactivity data, we have used MMPs as a consistent reference framework to identify sets of chemical replacements that either have the propensity to induce large-magnitude potency changes or tend to retain compound potency across diverse targets [3, 4]. Furthermore, we have extended the concept of MMPs to matched molecular series, i.e., analog series with different molecular core structures but corresponding substitution patterns [5, 6]. The identification of series with alternative core structures but similar SAR trends is highly relevant for lead optimization where SAR information from one series that has been explored historically is ideally used to guide compound design efforts for a new chemotype [6].

Authors’ Affiliations

Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA


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© Wassermann; licensee Chemistry Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.