Document Detail

Analysis and use of fragment-occurrence data in similarity-based virtual screening.
MedLine Citation:
PMID:  19536456     Owner:  NLM     Status:  MEDLINE    
Current systems for similarity-based virtual screening use similarity measures in which all the fragments in a fingerprint contribute equally to the calculation of structural similarity. This paper discusses the weighting of fragments on the basis of their frequencies of occurrence in molecules. Extensive experiments with sets of active molecules from the MDL Drug Data Report and the World of Molecular Bioactivity databases, using fingerprints encoding Tripos holograms, Pipeline Pilot ECFC_4 circular substructures and Sunset Molecular keys, demonstrate clearly that frequency-based screening is generally more effective than conventional, unweighted screening. The results suggest that standardising the raw occurrence frequencies by taking the square root of the frequencies will maximise the effectiveness of virtual screening. An upper-bound analysis shows the complex interactions that can take place between representations, weighting schemes and similarity coefficients when similarity measures are computed, and provides a rationalisation of the relative performance of the various weighting schemes.
Shereena M Arif; John D Holliday; Peter Willett
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't     Date:  2009-06-18
Journal Detail:
Title:  Journal of computer-aided molecular design     Volume:  23     ISSN:  1573-4951     ISO Abbreviation:  J. Comput. Aided Mol. Des.     Publication Date:  2009 Sep 
Date Detail:
Created Date:  2009-08-24     Completed Date:  2009-11-13     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  8710425     Medline TA:  J Comput Aided Mol Des     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  655-68     Citation Subset:  IM    
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, 211 Portobello Street, Sheffield, S1 4DP, UK.
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MeSH Terms
Databases, Factual
Drug Discovery / methods*
Holography / methods
Molecular Structure*
Pharmaceutical Preparations / chemistry,  classification
Quantitative Structure-Activity Relationship
Reg. No./Substance:
0/Pharmaceutical Preparations

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