Enhancing the effectiveness of fingerprint-based virtual screening: Use of turbo similarity searching and of fragment frequencies of occurrence

Shereena M. Arif, Jérôme Hert, John D. Holliday, Nurul Malim, Peter Willett

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Citations (Scopus)

Abstract

Binary fingerprints encoding the presence of 2D fragment substructures in molecules are extensively used for similarity-based virtual screening in the agrochemical and pharmaceutical industries. This paper describes two techniques for enhancing the effectiveness of screening: the use of a second-level search based on the nearest neighbours of the initial reference structure; and the use of weighted fingerprints encoding the frequency of occurrence, rather than just the mere presence, of substructures. Experiments using several databases for which both structural and bioactivity data are available demonstrate the effectiveness of these two approaches.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages404-414
Number of pages11
Volume5780 LNBI
DOIs
Publication statusPublished - 2009
Externally publishedYes
Event4th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2009 - Sheffield
Duration: 7 Sep 20099 Sep 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5780 LNBI
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other4th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2009
CitySheffield
Period7/9/099/9/09

Fingerprint

Virtual Screening
Substructure
Fingerprint
Screening
Fragment
Encoding
Pharmaceuticals
Bioactivity
Drug products
Nearest Neighbor
Molecules
Industry
Binary
Demonstrate
Experiment
Experiments
Similarity

Keywords

  • Chemoinformatics
  • Fingerprint
  • Fragment substructure
  • Similarity measure
  • Similarity searching
  • Turbo similarity searching
  • Virtual screening
  • Weighting scheme

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Arif, S. M., Hert, J., Holliday, J. D., Malim, N., & Willett, P. (2009). Enhancing the effectiveness of fingerprint-based virtual screening: Use of turbo similarity searching and of fragment frequencies of occurrence. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 5780 LNBI, pp. 404-414). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5780 LNBI). https://doi.org/10.1007/978-3-642-04031-3_35

Enhancing the effectiveness of fingerprint-based virtual screening : Use of turbo similarity searching and of fragment frequencies of occurrence. / Arif, Shereena M.; Hert, Jérôme; Holliday, John D.; Malim, Nurul; Willett, Peter.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 5780 LNBI 2009. p. 404-414 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5780 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Arif, SM, Hert, J, Holliday, JD, Malim, N & Willett, P 2009, Enhancing the effectiveness of fingerprint-based virtual screening: Use of turbo similarity searching and of fragment frequencies of occurrence. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 5780 LNBI, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5780 LNBI, pp. 404-414, 4th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2009, Sheffield, 7/9/09. https://doi.org/10.1007/978-3-642-04031-3_35
Arif SM, Hert J, Holliday JD, Malim N, Willett P. Enhancing the effectiveness of fingerprint-based virtual screening: Use of turbo similarity searching and of fragment frequencies of occurrence. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 5780 LNBI. 2009. p. 404-414. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-04031-3_35
Arif, Shereena M. ; Hert, Jérôme ; Holliday, John D. ; Malim, Nurul ; Willett, Peter. / Enhancing the effectiveness of fingerprint-based virtual screening : Use of turbo similarity searching and of fragment frequencies of occurrence. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 5780 LNBI 2009. pp. 404-414 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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