Why do we need so many chemical similarity search methods?
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Updated: Sep 27, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
Published on: June 6, 2025
Robert P Sheridan1, Simon K Kearsley
1Dept of Molecular Systems, RY50SW-100 Merck Research Laboratories, Rahway, NJ 07065, USA. sheridan@merck.com
Abstract:
Computational tools to search chemical structure databases are essential to finding leads early in a drug discovery project. Similarity methods are among the most diverse and most useful. We will present some lessons we have gathered over many years experience with in-house methods on several therapeutic problems. The effectiveness of any similarity method can vary greatly from one biological activity to another in a way that is difficult to predict. Also, any two methods tend to select different subsets of actives from a database, so it is advisable to use several search methods where possible.
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