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pharmacophore

pharmacophore. Megon Walker Bioinformatics Program Boston University. prioritization of chemical libraries. high-throughput screening. Proceedings of the Fifteenth International Conference on Machine Learning, 1998:1-9. J. Chem Inf. Comput. Sci. 2003, 43: 667-673. compound datasets.

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pharmacophore

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  1. pharmacophore Megon Walker Bioinformatics Program Boston University

  2. prioritization of chemical libraries • high-throughput screening Proceedings of the Fifteenth International Conference on Machine Learning, 1998:1-9. J. Chem Inf. Comput. Sci. 2003, 43: 667-673.

  3. compound datasets NIH/NCI developmental therapeutics program (DTP) human tumor cell line screen • cancer screen of 43,000 compounds • compounds tested at 5 different concentrations for the ability to inhibit 60 different human tumor cell lines • dose response data • 3 concentration parameters • GI50 • TGI • LC50 • MDL's SDFile format(2D structure) http://dtp.nci.nih.gov/docs/cancer/cancer_data.html DuPont KDD thrombin dataset • 632 DuPont thrombin-targeting compounds • 149 actives • 483 inactives • a binary feature vector for each compound with 1 of 2 class labels • shaped-based features • pharmacophore features • 139,351 features J Mol Graph Model. 2002 Jun;20(6):469-77. J Chem Inf Comput Sci. 2002 Sep-Oct;42(5):1230-40. KDD Cup 2001. http://www.cs.wisc.edu/~dpage/kddcup2001/

  4. pharmacophore derivation • J Med Chem. 2004 Dec 2;47(25):6144-59.

  5. pharmacophore derivation • Curr Med Chem. 2004 Jan;11(1):71-90.

  6. pharmacophore derivation • J Med Chem. 1999 Aug 26;42(17):3251-64. • Curr Med Chem. 2004 Jan;11(1):71-90.

  7. pharmacophore and screening • Biogen: • bit string representation of 3D binding interactions used to filter compounds during virtual screening (docking) • J Med Chem. 2004, 47: 337-344. • Deltagen: • machine learning and information theory to identify pharmacophore ensembles for compound classification • J Chem Inf Comput Sci. 2003, 43: 47-54; 2163-2169. • Novartis • naïve Bayes classifier for ranking & enrichment of HTD/HTS results • J Med Chem. 2004, 47: 2743-2749, 4356-4359, 6144-6159. J Chem Inf Comput Sci. 2004, 44:993-9.

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