Computation of the physio-chemical properties and data mining of large molecular collections

Journal of Computational Chemistry
Ailan ChengK M Merz

Abstract

Very large data sets of molecules screened against a broad range of targets have become available due to the advent of combinatorial chemistry. This information has led to the realization that ADME (absorption, distribution, metabolism, and excretion) and toxicity issues are important to consider prior to library synthesis. Furthermore, these large data sets provide a unique and important source of information regarding what types of molecular shapes may interact with specific receptor or target classes. Thus, the requirement for rapid and accurate data mining tools became paramount. To address these issues Pharmacopeia, Inc. formed a computational research group, The Center for Informatics and Drug Discovery (CIDD).* In this review we cover the work done by this group to address both in silico ADME modeling and data mining issues faced by Pharmacopeia because of the availability of a large and diverse collection (over 6 million discrete compounds) of drug-like molecules. In particular, in the data mining arena we discuss rapid docking tools and how we employ them, and we describe a novel data mining tool based on a ID representation of a molecule followed by a molecular sequence alignment step. For the ADME area we discuss the...Continue Reading

References

Dec 1, 1992·Journal of Computer-aided Molecular Design·H J Böhm
Oct 1, 1991·Journal of Computer-aided Molecular Design·A Y Meyer, W G Richards
Jan 1, 1990·Proteins·D S Goodsell, A J Olson
Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Oct 25, 1982·Journal of Molecular Biology·I D KuntzT E Ferrin
Dec 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·M H OhlmeyerW C Still
Jun 1, 1995·Journal of Computer-aided Molecular Design·D FrenkelD R Westhead
Jul 1, 1995·Clinical Pharmacology and Therapeutics·J A DiMasi
Sep 1, 1994·Journal of Pharmaceutical Sciences·M H AbrahamR C Mitchell
Jul 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·E T BaldwinJ W Erickson
Aug 2, 1996·Journal of Medicinal Chemistry·R D CramerA M Ferguson
Jan 1, 1996·Medicinal Research Reviews·R S BohacekW C Guida
Mar 14, 1997·Journal of Medicinal Chemistry·M C NicklausY Pommier
Apr 4, 1997·Journal of Molecular Biology·G JonesR Taylor
May 8, 1998·Journal of Neurochemistry·W M Pardridge
Aug 28, 1998·Journal of Medicinal Chemistry·A AjayM A Murcko
Dec 3, 1998·Journal of Computer-aided Molecular Design·M Rarey, J S Dixon
Jul 27, 1999·Current Opinion in Chemical Biology·D A Smith, H van de Waterbeemd
Jul 27, 1999·Current Opinion in Chemical Biology·W P WaltersM A Murcko
Sep 14, 1999·Journal of Computer-aided Molecular Design·P A Hunt
Sep 14, 1999·Journal of Computer-aided Molecular Design·S L Dixon, H O Villar
Jan 19, 2000·Pharmaceutical Science & Technology Today·I GroverI Bakshi
Feb 9, 2000·Pharmaceutical Science & Technology Today·I GroverI Bakshi
Feb 12, 2000·Journal of Medicinal Chemistry·D LeungD P Fairlie
Apr 13, 2000·Journal of Chemical Information and Computer Sciences·D J Livingstone
Oct 29, 2000·Journal of Medicinal Chemistry·W J EganJ J Baldwin
Jan 6, 2001·Journal of Molecular Graphics & Modelling·P Labute
Jun 1, 1998·Analytical Chemistry·W J Egan, S L Morgan

❮ Previous
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Citations

Mar 30, 2002·Advanced Drug Delivery Reviews·William J Egan, Georgio Lauri
Jan 28, 2003·Drug Discovery Today·Robert P Sheridan, Simon K Kearsley
Sep 10, 2003·Drug Discovery Today·Hongshi Yu, Adedayo Adedoyin
May 13, 2009·Molecular Pharmaceutics·Adam C ChamberlinDonald G Truhlar
Oct 6, 2010·The Pharmacogenomics Journal·T M Baye, R A Wilke
Feb 28, 2013·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Prakash RadhakrishnanAmarnath Natarajan
Aug 29, 2014·International Journal of Molecular Sciences·Bingjie HuDaisuke Kihara
Dec 29, 2004·Journal of Drug Targeting·Paul R LockmanDavid D Allen
Aug 23, 2006·Expert Opinion on Drug Metabolism & Toxicology·Sean EkinsTatiana Nikolskaya
Jan 4, 2012·Journal of Pharmaceutical Sciences·Pooja Naik, Luca Cucullo
Aug 25, 2004·European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences·Annika MälkiäKyösti Kontturi
Nov 2, 2011·Seminars in Cell & Developmental Biology·Hui Miao, Bingcheng Wang
May 6, 2009·Angewandte Chemie·Hans-Jörg Schneider
Jun 28, 2007·Journal of Chemical Information and Modeling·Anthony E Klon, David J Diller
Jan 7, 2005·Journal of Medicinal Chemistry·Raveendra DayamNouri Neamati

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