An Adaptive Reference Point Approach to Efficiently Search Large Chemical Databases

  • Francesco NapolitanoEmail author
  • Roberto Tagliaferri
  • Pierre Baldi
Part of the Smart Innovation, Systems and Technologies book series (SIST, volume 26)


The ability to rapidly search large repositories of molecules is a crucial task in chemoinformatics. In this work we propose AOR, an approach based on adaptive reference points to improve state of the art performances in querying large repositories of binary fingerprints basing on the Tanimoto distance. We propose a unifying view between the context of reference points and the previously proposed hashing techniques. We also provide a mathematical model to forecast and generalize the results, that is validated by simulating queries over an excerpt of the ChemDB. Clustering techniques are finally introduced to improve the performances. For typical situations the proposed algorithm is shown to resolve queries up to 4 times faster than compared methods.


molecular fingerprits chemical database binary vector search 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Irwin, J.J., Shoichet, B.K.: ZINC–A Free Database of Commercially Available Compounds for Virtual Screening. Journal of Chemical Information and Computer Sciences 45, 177–182 (2005)CrossRefGoogle Scholar
  2. 2.
    Chen, J., Linstead, E., Swamidass, S.J., Wang, D., Baldi, P.: ChemDB Update–Full Text Search and Virtual Chemical Space. Bioinformatics 23, 2348–2351 (2007)CrossRefGoogle Scholar
  3. 3.
    Wang, Y., Xiao, J., Suzek, T., Zhang, J., Wang, J., Bryant, S.: PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Research 37, W623–W633 (2009)Google Scholar
  4. 4.
    Sayers, E., Barrett, T., Benson, D., Bolton, E., Bryant, S., Canese, K., Chetvernin, V., Church, D., DiCuccio, M., Federhen, S., et al.: Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 38, D5–D16 (2010)Google Scholar
  5. 5.
    Benz, R.W., Swamidass, S.J., Baldi, P.: Discovery of Power-Laws in Chemical Space. Journal of Chemical Information and Modeling 48, 1138–1151 (2008)CrossRefGoogle Scholar
  6. 6.
    Paris, R.B.: Incomplete beta functions. In: Olver, F.W.J., Lozier, D.M., Boisvert, R.F., et al. (eds.) NIST Handbook of Mathematical Functions. Cambridge University Press (2010) ISBN 978-0521192255Google Scholar
  7. 7.
    Shapiro, M.: The choice of reference points in best-match file searching. Communications of the ACM 20, 339–343 (1977)CrossRefGoogle Scholar
  8. 8.
    Nasr, R., Hirschberg, D.S., Baldi, P.: Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors. J. Chem. Inf. Model. 50(8), 1358–1368 (2010), doi:10.1021/ci100132gCrossRefGoogle Scholar
  9. 9.
    Bohacek, R.S., McMartin, C., Guida, W.C.: The art and practice of structure-based drug design: A molecular modelling perspective. Medicinal Research Reviews 16(1), 3–50 (1996)CrossRefGoogle Scholar
  10. 10.
    Swamidass, S.J., Baldi, P.: Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time. Journal of Chemical Information and Modeling 47(2), 302–317 (2007)CrossRefGoogle Scholar
  11. 11.
    Baldi, P., Hirschberg, D.S.: An Intersection Inequality Sharper than the Tanimoto Triangle Inequality for Efficiently Searching Large Databases. J. Chem. Inf. Model. 49(8), 1866–1870 (2009), doi:10.1021/ci900133jCrossRefGoogle Scholar
  12. 12.
    Burkhard, W.A., Keller, R.M.: Some approaches to best-match file searching. Communications of the ACM Archive 16(4), 230–236 (1973)CrossRefzbMATHGoogle Scholar
  13. 13.
    Chen, J.H., Linstead, E., Swamidass, S.J., Wang, D., Baldi, P.: ChemDB update–full-text search and virtual chemical space. Bioinformatics 23(17), 2348–2351 (2007)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Francesco Napolitano
    • 1
    • 2
    Email author
  • Roberto Tagliaferri
    • 1
  • Pierre Baldi
    • 2
  1. 1.Department of InformaticsUniversity of SalernoFiscianoItaly
  2. 2.Institute for Genomics and Bioinformatics, School of Information and Computer SciencesUniversity of California-IrvineIrvineUSA

Personalised recommendations