Bayesian screening for active compounds in high-dimensional chemical spaces combining property descriptors and molecular fingerprints

Chemical Biology and Drug Design

Volumn 71, Issue 1, 2008, Pages 8-14

  Vogt, Martin ^a   Bajorath, Jürgen ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

Active compounds; Bayesian modeling; High dimensional chemical spaces; Molecular fingerprints; Property descriptors; Similarity searching; Virtual screening

Indexed keywords

CHEMICAL COMPOUND;

ARTICLE; BAYES THEOREM; BIOLOGICAL ACTIVITY; CALCULATION; CHEMICAL STRUCTURE; CORRELATION ANALYSIS; DATA BASE; DRUG SCREENING; METHODOLOGY; MOLECULE; PARAMETER; PRIORITY JOURNAL; PROBABILITY; PROPERTY DESCRIPTOR; QUANTITATIVE ANALYSIS; SIMILARITY SEARCHING; STRUCTURE ACTIVITY RELATION;

BAYES THEOREM; DATABASES, FACTUAL; DRUG EVALUATION, PRECLINICAL;

EID: 37849002814     PISSN: 17470277     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2007.00602.x     Document Type: Article

References (18)

1. Duda R.O., Hart P.E., Stork D.G. (2000) Pattern Classification, 2nd edn. New York : Wiley-Interscience.
2. Xia X., Maliski E.G., Gallant P., Rogers D. (2004) Classification of kinase inhibitors using a Bayesian model. J Med Chem 47 : 4463 4470.
3. Bender A., Mussa Y., Glen R.C., Reiling S. (2004) Molecular similarity searching using atom environments, information-based feature selection, and a naïve Bayesian classifier. J Chem Inf Comput Sci 44 : 170 178.
4. Glick M., Jenkins J.L., Nettles J.H., Hitchings H., Davies J.W. (2006) Enrichment of high-throughput screening data with increasing levels of noise using support vectors machines, recursive partitioning, and Laplacian-modified naïve Bayesian classifiers. J Chem Inf Model 46 : 193 200.
5. Paolini G.V., Shapland R.H.B., van Hoorn W.P., Mason J.S., Hopkins A.L. (2006) Global mapping of pharmacological space. Nat Biotechnol 24 : 805 815.
6. Godden J.W., Bajorath J. (2006) A distance function for retrieval of active molecules from complex chemical space representations. J Chem Inf Model 46 : 1094 1097.
7. Vogt M., Godden J.W., Bajorath J. (2007) Bayesian interpretation of a distance function for navigating high-dimensional descriptor spaces. J Chem Inf Model 47 : 39 46.
8. Kullback S. (1997) Information Theory and Statistics. Mineola : Dover Publications.
9. Vogt M., Bajorath J. (2007) Introduction of an information-theoretic method to predict recovery rates of active compounds for Bayesian in silico screening: theory and screening trials. J Chem Inf Model 47 : 337 341.
10. Vogt M., Bajorath J. (2007) Introduction of a generally applicable method to estimate retrieval of active molecules for similarity searching using fingerprints. ChemMedChem 2 : 1311 1320.
11. Zhang H. (2004) The optimality of naïve Bayes. In : Proceedings of the Seventeenth Florida Artificial Intelligence Research Society Conference. Menlo Park : The AAAI Press p. 562 567.
12. John H.J., Langley P. (1995) Estimating continuous distributions in Bayesian classifiers. In : Proceedings of the Eleventh Conference on Uncertainty in Artificial Intelligence. San Mateo : Morgan Kaufmann Publishers p. 338 345.
13. Xue L., Godden J.W., Bajorath J. (2003) Mini-fingerprints for virtual screening: design principles and generation of novel prototypes based on information theory. SAR QSAR Environ Res 14 : 27 40.
14. Xue L., Godden J.W., Stahura F.L., Bajorath J. (2003) Design and evaluation of a molecular fingerprint involving the transformation of property descriptor values into a binary classification scheme. J Chem Inf Comput Sci 43 : 1151 1157.
15. Whitley D.C., Ford M.G., Livingstone D.J. (2000) Unsupervised forward selection: a method for eliminating redundant variables. J Chem Inf Comput Sci 40 : 1160 1168.
16. Irwin J.J., Shoichet B.K. (2005) ZINC - A free database of commercially available compounds for virtual screening. J Chem Inf Model 45 : 177 182.
17. Schuffenhauer A., Floersheim P., Acklin P., Jacoby E. (2003) Similarity metrics for ligands reflecting the similarity of the target protein. J Chem Inf Comput Sci 43 : 391 405.
18. Willett P. (2005) Searching techniques for databases of two- and three-dimensional structures. J Med Chem 48 : 4183 4199.