Skip to content
Research Article Open access CC BY 3.0

Molecular Similarity Searching Method Based on Adaptive IR Technique

Mohammed Salem Binwahlan, Naomie Salim

Chemical Science International Journal · pp. 787–797 · Published 31 May 2014

10.9734/ACSJ/2014/10175

Abstract

An age-old question remains as an open research problem in the field of chemoinformatics, which is how much could the proposed approach enhance the effectiveness of lead-discovery programmes? Answering that question is a target of any new virtual screening approach. The current research tries to contribute in this direction by improving the performance of molecular similarity searching process. In this paper, Okapi similarity measure, which is effective and widely used in text retrieval, is adapted to perform the role of molecular similarity measure in 2D fingerprints. The adapted similarity measure calculates the molecular similarity between a reference structure and a database structure. The experimental results showed that the proposed method performs well compared to Tanimoto coefficient.  

Molecular similarity searching structure searching similarity coefficients virtual screening

References (21)

  1. 1 Chemical Similarity Searching [DOI]
  2. 2 Concepts and applications of molecular similarity
  3. 3 Atom pairs as molecular features in structure-activity studies: definition and applications [DOI]
  4. 4 Virtual screening—an overview [DOI]
  5. 5 Molecular Similarity in Medicinal Chemistry [DOI]
  6. 6 Similarity maps - a visualization strategy for molecular fingerprints and machine-learning methods [DOI]
  7. 7 New Methods for Ligand-Based Virtual Screening: Use of Data Fusion and Machine Learning to Enhance the Effectiveness of Similarity Searching [DOI]
  8. 8 Chemoinformatics Approaches to Virtual Screening [DOI]
  9. 9 Combinatorial Preferences Affect Molecular Similarity/Diversity Calculations Using Binary Fingerprints and Tanimoto Coefficients [DOI]
  10. 10 Molecular substructure similarity searching: efficient retrieval in two-dimensional structure databases [DOI]
  11. 11 Introduction to Similarity Searching in Chemistry
  12. 12 New Fragment Weighting Scheme for the Bayesian Inference Network in Ligand-Based Virtual Screening [DOI]
  13. 13 Virtual Screening for Bioactive Molecules [DOI]
  14. 14 Implementation of nearest-neighbor searching in an online chemical structure search system [DOI]
  15. 15 Similarity and Dissimilarity Methods for Processing Chemical Structure Databases [DOI]
  16. 16 Similarity‐Based Virtual Screening with a Bayesian Inference Network [DOI]
  17. 17 Similarity searching on CAS Registry substances. 1. Global molecular property and generic atom triangle geometric searching [DOI]
  18. 18 Evaluation of a Bayesian inference network for ligand-based virtual screening [DOI]
  19. 19 Intelligent fusion of structural and citation-based evidence for text classification [DOI]
  20. 20 Digital libraries in chemistry: providing access to chemical structure information
  21. 21 Chemoinformatics: A Textbook [DOI]

Cited by 0

No indexed citations yet.

Article metrics

Real usage data collected on this platform.

0

Page views

0

PDF downloads

0

Outbound clicks

0

Citations

Views by country

Approximate, from request IP at view time — not citizenship or institution. Countries with fewer than 5 views are grouped as "Other".

No views recorded yet.

Traffic sources

Referring site, by host.

No traffic recorded yet.

Views and downloads exclude known bots/crawlers. Citations combines this platform's own DOI-resolved index with each external source's own reported total — see Cited by above for individually listed citing works. Last refreshed 0 seconds ago.