Future Medicinal ChemistryVol. 4, No. 15 CommentaryComputational chemistry and drug discovery: a call to actionJohanna M Jansen, Rommie E Amaro, Wendy Cornell, Y Jane Tseng & W Patrick WaltersJohanna M Jansen* Author for correspondenceNovartis Institutes for Biomedical Research, Global Discovery Chemistry/Oncology, Infectious Diseases, & Exploratory Chemistry, Emeryville, CA 94608, USA. , Rommie E AmaroDepartment of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA, Wendy CornellMerck Research Labs, Knowledge Discovery/Knowledge Management, Rahway, NJ 07065, USA, Y Jane TsengGraduate Institute of Biomedical Electronics & Bioinformatics, National Taiwan University, Taipei, Taiwan & W Patrick WaltersVertex Pharmaceuticals Inc., Cambridge, MA 02139, USAPublished Online:22 Oct 2012https://doi.org/10.4155/fmc.12.137AboutSectionsView ArticleView Full TextPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareShare onFacebookTwitterLinkedInReddit View articleKeywords: collaborationcomputational chemistrydrug discoveryeducationreproducibilityTeach-Discover-TreatReferences1 Jorgensen WL. The many roles of computation in drug discovery. Science303(5665),1813–1818 (2004).Crossref, Medline, CAS, Google Scholar2 Jansen JM, Cornell W, Tseng YJ, Amaro RE. Teach-Discover-Treat (TDT): collaborative drug discovery for neglected diseases. J. Mol. Graph. Model. doi: 10.1016/j.jmgm.2012.07.007 (2012) (In Press).Medline, Google Scholar3 Guiguemde WA, Shelat AA, Garcia-Bustos JF, Diagana TT, Gamo FJ, Guy RK. Global phenotypic screening for antimalarials. Chem.Biol.19(1),116–129 (2012).Crossref, Medline, CAS, Google Scholar4 Lessl M, Bryans JS, Richards D, Asadullah K. Crowd sourcing in drug discovery. Nat. Rev. Drug Discov.10(4),241–242 (2011).Crossref, Medline, CAS, Google Scholar5 Norman TC, Bountra C, Edwards AM, Yamamoto KR, Friend SH. Leveraging crowdsourcing to facilitate the discovery of new medicines. Sci. Transl. Med.3(88),88mr1 (2011).Crossref, Medline, Google Scholar6 Strauss S. Pharma embraces open source models. Nat. Biotechnol.28(7),631–634 (2010).Crossref, Medline, CAS, Google Scholar7 Cross JB, Thompson DC, Rai BK et al. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J. Chem. Inf. Model.49(6),1455–1474 (2009).Crossref, Medline, CAS, Google Scholar8 McGaughey GB, Sheridan RP, Bayly CI et al. Comparison of topological, shape, and docking methods in virtual screening. J.Chem. Inf. Model.47(4),1504–1519 (2007).Crossref, Medline, CAS, Google Scholar9 Cummings MD, DesJarlais RL, Gibbs AC, Mohan V, Jaeger EP. Comparison of automated docking programs as virtual screening tools. J. Med.Chem.48(4),962–976 (2005).Crossref, Medline, CAS, Google Scholar10 Perola E, Walters WP, Charifson PS. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins56(2),235–249 (2004).Crossref, Medline, CAS, Google Scholar11 Cornell WD. Recent evaluations of high throughput docking methods for pharmaceutical lead finding – consensus and caveats. Annu. Rep. Comput. Chem.2,297–323 (2006).Crossref, CAS, Google Scholar12 Boyd DR. How computational chemistry became important in the pharmaceutical industry. In: Reviews in Computational Chemistry. Lipkowitz DB, Cundari TR (Eds). John Wiley and Sons, Inc., London, UK, 401–451 (2007).Google Scholar13 Bourne PE. What do I want from the publisher of the future?. PLoS Comput.Biol.6(5),e1000787 (2010).Crossref, Medline, Google Scholar14 Dunbar JB Jr, Smith RD, Yang CY et al. CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. J. Chem. Inf. Model.51(9),2036–2046 (2011).Crossref, Medline, CAS, Google Scholar101 Teach-Discover-Treat. www.teach-discover-treat.orgGoogle Scholar102 Bill and Melinda Gates foundation. Private and Public Partners Unite to Combat 10 Neglected Tropical Diseases by 2020. www.gatesfoundation.org/press-releases/pages/combating-10-neglected-tropical-diseases-120130.aspxCrossref, Google Scholar103 ChEMBL database. www.ebi.ac.uk/chembldbGoogle Scholar104 Collaborative drug discovery. www.collaborativedrug.comGoogle Scholar105 PubChem. http://pubchem.ncbi.nlm.nih.govGoogle Scholar106 Source Forge. http://sourceforge.netGoogle Scholar107 Open Babel. http://openbabel.orgGoogle Scholar108 Chemistry Development Kit. http://sourceforge.net/apps/mediawiki/cdkGoogle Scholar109 RDKit. Cheminformatics and Machine Learning Software. www.rdkit.orgGoogle Scholar110 Indigo toolkit. http://ggasoftware.com/opensource/indigoGoogle Scholar111 Groovy cheminformatics with the chemistry development kit. www.lulu.com/shop/egon-willighagen/groovy-cheminformatics-with-the-chemistry-development-kit/paperback/product-20267607.htmlGoogle Scholar112 How to use Jmol to study and present molecular structures. http://books.google.com/books?id=59kQFyfbsJMCGoogle Scholar113 Open Babel. Official user guide. www.lulu.com/shop/open-babel-developers/open-babel/paperback/product-14927363.htmlGoogle Scholar114 Chemistry Toolkit Rosetta Wiki. http://ctr.wikia.com/wiki/Chemistry_Toolkit_Rosetta_WikiGoogle Scholar115 PLoS journals. www.plos.org/publications/journalsGoogle Scholar116 Teach-Discover-Treat. Competition details. www.teach-discover-treat.org/details-for-the-competitionGoogle ScholarFiguresReferencesRelatedDetailsCited ByThe Synthesis and Anti-inflammatory Studies of New Pyrimidine Derivatives, Inhibitors of Cyclooxygenase Isoforms23 September 2022 | Russian Journal of Bioorganic Chemistry, Vol. 48, No. 5CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding15 February 2022 | Nature Reviews Chemistry, Vol. 6, No. 4Convolutional neural network scoring and minimization in the D3R 2017 community challenge10 July 2018 | Journal of Computer-Aided Molecular Design, Vol. 33, No. 1Antibiotics: where to throw the spanner in the ribosomal machinery?Samuel A McKie21 September 2016 | Future Medicinal Chemistry, Vol. 8, No. 16 Vol. 4, No. 15 Follow us on social media for the latest updates Metrics Downloaded 475 times History Published online 22 October 2012 Published in print October 2012 Information© Future Science LtdKeywordscollaborationcomputational chemistrydrug discoveryeducationreproducibilityTeach-Discover-TreatFinancial & competing interests disclosureRE Amaro is supported in part by the National Institutes of Health through the NIH Director's New Innovator Award Program DP2-OD007237. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.No writing assistance was utilized in the production of this manuscript.PDF download
No takes yet. Share an insight, caveat, or question.
Jansen et al. (2012) studied this question.
Synapse has enriched 5 closely related papers on similar clinical questions. Consider them for comparative context: