Molecular Diversity

, Volume 10, Issue 3, pp 389–403 | Cite as

Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers

  • Aurélien Monge
  • Alban Arrault
  • Christophe Marot
  • Luc Morin-Allory
Full–length paper


The data for 3.8 million compounds from structural databases of 32 providers were gathered and stored in a single chemical database. Duplicates are removed using the IUPAC International Chemical Identifier. After this, 2.6 million compounds remain. Each database and the final one were studied in term of uniqueness, diversity, frameworks, ‘drug-like’ and ‘lead–like’ properties. This study also shows that there are more than 87 000 frameworks in the database. It contains 2.1 million ‘drug-like’ molecules among which, more than one million are ‘lead-like’. This study has been carried out using ‘ScreeningAssistant’, a software dedicated to chemical databases management and screening sets generation. Compounds are stored in a MySQL database and all the operations on this database are carried out by Java code. The druglikeness and leadlikeness are estimated with ‘in–house’ scores using functions to estimate convenience to properties; unicity using the InChI code and diversity using molecular frameworks and fingerprints. The software has been conceived in order to facilitate the update of the database. ‘ScreeningAssistant’ is freely available under the GPL license.

Key words

chemical databases chemoinformatics diversity drug-like lead-like screening 



H bond acceptor


H bond donor


high-throughput screening


IUPAC International Chemical Identifier


Java Native Interface


molecular weight




stochastic clustering analysis


smallest set of smallest rings


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Copyright information

© Springer Science + Business Media, Inc. 2006

Authors and Affiliations

  • Aurélien Monge
    • 1
  • Alban Arrault
    • 1
  • Christophe Marot
    • 1
  • Luc Morin-Allory
    • 1
  1. 1.Institut de Chimie Organique et Analytique, UMR CNRS 6005Université d’OrléansOrléans Cedex 2France

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