John Irwin, PhD
Adjunct Professor
Pharmaceutical Chemistry
School of Pharmacy

Websites

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• @@chem4biology on Twitter (twitter.com)
• ZINC Database of compounds for ligand discovery (zinc.docking.org)
• Irwin Lab (irwinlab.compbio.ucsf.edu)
• Benchmarks for Molecular Docking (dude.docking.org)
• ZINC15 (zinc15.docking.org)
• Targets of compounds by the Similarity Ensemble Approach (sea.docking.org)
• Molecular Excipients (with CERSI/FDA) (excipients.ucsf.bkslab.org)
• DOCK Blaster, free online virtual screening (blaster.docking.org)

Videos

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• How to acquire a screening library for docking (youtube.com)

Grants and Projects

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• A Web-Based Automatic Virtual Screening System, NIH, 2004-2025
• Ultra-large library docking for ligand discovery, NIH, 2019-2023

Publications (100)

Top publication keywords:
Models, MolecularLigandsDopamine AgonistsPharmaceutical PreparationsDrug Evaluation, PreclinicalDatabases, ChemicalSmall Molecule LibrariesDrug DiscoveryBenchmarkingDrug DesignZincbeta-Lactamase InhibitorsMolecular Docking SimulationDatabases, FactualProteins

• Structure-based discovery of CFTR potentiators and inhibitors.
  bioRxiv : the preprint server for biology 2024 Liu F, Kaplan AL, Levring J, Einsiedel J, Tiedt S, Distler K, Omattage NS, Kondratov IS, Moroz YS, Pietz HL, Irwin JJ, Gmeiner P, Shoichet BK, Chen J
• Small vs. Large Library Docking for Positive Allosteric Modulators of the Calcium Sensing Receptor.
  bioRxiv : the preprint server for biology 2024 Liu F, Wu CG, Tu CL, Glenn I, Meyerowitz J, Levit Kaplan A, Lyu J, Cheng Z, Tarkhanova OO, Moroz YS, Irwin JJ, Chang W, Shoichet BK, Skiniotis G
• Large library docking for cannabinoid-1 receptor agonists with reduced side effects.
  bioRxiv : the preprint server for biology 2024 Tummino TA, Iliopoulos-Tsoutsouvas C, Braz JM, O'Brien ES, Stein RM, Craik V, Tran NK, Ganapathy S, Liu F, Shiimura Y, Tong F, Ho TC, Radchenko DS, Moroz YS, Rosado SR, Bhardwaj K, Benitez J, Liu Y, …
• Docking for molecules that bind in a symmetric stack to Alzheimer’s disease tau fibrils with SymDOCK.
  Biophysical Journal 2024 Matthew S. Smith, Peter Kunach, Ian S. Knight, Rian Kormos, Joseph G. Pepe, Isabella Glenn, John J. Irwin, William F. DeGrado, Marc I. Diamond, Sarah H. Shahmoradian, Brian K. Shoichet
• DockOpt: A Tool for Automatic Optimization of Docking Models.
  Journal of chemical information and modeling 2024 Knight IS, Mailhot O, Tang KG, Irwin JJ

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• Docking for Molecules That Bind in a Symmetric Stack with SymDOCK.
  Journal of chemical information and modeling 2024 Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK
• AlphaFold2 structures template ligand discovery.
  bioRxiv : the preprint server for biology 2023 Lyu J, Kapolka N, Gumpper R, Alon A, Wang L, Jain MK, Barros-Álvarez X, Sakamoto K, Kim Y, DiBerto J, Kim K, Tummino TA, Huang S, Irwin JJ, Tarkhanova OO, Moroz Y, Skiniotis G, Kruse AC, Shoichet BK, …
• Docking for EP4R antagonists active against inflammatory pain.
  Nature communications 2023 Gahbauer S, DeLeon C, Braz JM, Craik V, Kang HJ, Wan X, Huang XP, Billesbølle CB, Liu Y, Che T, Deshpande I, Jewell M, Fink EA, Kondratov IS, Moroz YS, Irwin JJ, Basbaum AI, Roth BL, Shoichet BK
• Docking for molecules that bind in a symmetric stack with SymDOCK.
  bioRxiv : the preprint server for biology 2023 Smith MS, Knight IS, Kormos RC, Pepe JG, Kunach P, Diamond MI, Shahmoradian SH, Irwin JJ, DeGrado WF, Shoichet BK
• Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.
  Protein science : a publication of the Protein Society 2023 Fink EA, Bardine C, Gahbauer S, Singh I, Detomasi TC, White K, Gu S, Wan X, Chen J, Ary B, Glenn I, O'Connell J, O'Donnell H, Fajtová P, Lyu J, Vigneron S, Young NJ, Kondratov IS, Alisoltani A, Simons…
• Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase.
  Journal of medicinal chemistry 2023 Singh I, Li F, Fink EA, Chau I, Li A, Rodriguez-Hernández A, Glenn I, Zapatero-Belinchón FJ, Rodriguez ML, Devkota K, Deng Z, White K, Wan X, Tolmachova NA, Moroz YS, Kaniskan HÜ, Ott M, García-Sastre…
• Structure-based discovery of conformationally selective inhibitors of the serotonin transporter.
  Cell 2023 Singh I, Seth A, Billesbølle CB, Braz J, Rodriguiz RM, Roy K, Bekele B, Craik V, Huang XP, Boytsov D, Pogorelov VM, Lak P, O'Donnell H, Sandtner W, Irwin JJ, Roth BL, Basbaum AI, Wetsel WC, Manglik A,…
• Large-Scale Docking in the Cloud.
  Journal of chemical information and modeling 2023 Tingle BI, Irwin JJ
• ZINC-22─A Free Multi-Billion-Scale Database of Tangible Compounds for Ligand Discovery.
  Journal of chemical information and modeling 2023 Tingle BI, Tang KG, Castanon M, Gutierrez JJ, Khurelbaatar M, Dandarchuluun C, Moroz YS, Irwin JJ
• Modeling the expansion of virtual screening libraries.
  Nature chemical biology 2023 Lyu J, Irwin JJ, Shoichet BK
• Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko DS, Moroz YS, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, …
• Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor.
  Science (New York, N.Y.) 2022 Fink EA, Xu J, Hübner H, Braz JM, Seemann P, Avet C, Craik V, Weikert D, Schmidt MF, Webb CM, Tolmachova NA, Moroz YS, Huang XP, Kalyanaraman C, Gahbauer S, Chen G, Liu Z, Jacobson MP, Irwin JJ, …
• Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity.
  Nature 2022 Kaplan AL, Confair DN, Kim K, Barros-Álvarez X, Rodriguiz RM, Yang Y, Kweon OS, Che T, McCorvy JD, Kamber DN, Phelan JP, Martins LC, Pogorelov VM, DiBerto JF, Slocum ST, Huang XP, Kumar JM, Robertson …
• Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2.
  bioRxiv : the preprint server for biology 2022 Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko D, Moroz Y, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, …
• Drug building blocks and libraries at risk in Ukraine.
  Science (New York, N.Y.) 2022 Kondratov IS, Moroz YS, Irwin JJ, Shoichet BK
• CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding.
  Nature reviews. Chemistry 2022 Ackloo S, Al-Awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, Bengio Y, Betz UAK, Bologa CG, Chodera JD, Cornell WD, Dunham I, Ecker GF, Edfeldt K, Edwards AM, Gilson MK, Gordijo CR, Hessler G, …
• Publisher Correction: A practical guide to large-scale docking.
  Nature protocols 2022 Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK
• Structures of the σ2 receptor enable docking for bioactive ligand discovery.
  Nature 2021 Alon A, Lyu J, Braz JM, Tummino TA, Craik V, O'Meara MJ, Webb CM, Radchenko DS, Moroz YS, Huang XP, Liu Y, Roth BL, Irwin JJ, Basbaum AI, Shoichet BK, Kruse AC
• A practical guide to large-scale docking.
  Nature protocols 2021 Bender BJ, Gahbauer S, Luttens A, Lyu J, Webb CM, Stein RM, Fink EA, Balius TE, Carlsson J, Irwin JJ, Shoichet BK
• Ligand Strain Energy in Large Library Docking.
  Journal of chemical information and modeling 2021 Gu S, Smith MS, Yang Y, Irwin JJ, Shoichet BK
• Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
  Science advances 2021 Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N,…
• Property-Unmatched Decoys in Docking Benchmarks.
  Journal of chemical information and modeling 2021 Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ
• Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking.
  bioRxiv : the preprint server for biology 2020 Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Martins LC, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, …
• ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery.
  Journal of chemical information and modeling 2020 Irwin JJ, Tang KG, Young J, Dandarchuluun C, Wong BR, Khurelbaatar M, Moroz YS, Mayfield J, Sayle RA
• The activities of drug inactive ingredients on biological targets.
  Science (New York, N.Y.) 2020 Pottel J, Armstrong D, Zou L, Fekete A, Huang XP, Torosyan H, Bednarczyk D, Whitebread S, Bhhatarai B, Liang G, Jin H, Ghaemi SN, Slocum S, Lukacs KV, Irwin JJ, Berg EL, Giacomini KM, Roth BL, …
• In vivo Efficacy of Novel Type Preferring MT1 Melatonin Receptor Inverse Agonists in C3H/HeN Mouse Models of Chronobiological Behavior.
  The FASEB Journal 2020 Grant Glatfelter, Reed Stein, Hye Jin Kang, Anthony Jones, John Irwin, Bryan Roth, Brian Shoichet, Margarita Dubocovich
• Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.
  Journal of the American Chemical Society 2020 Wan X, Yang T, Cuesta A, Pang X, Balius TE, Irwin JJ, Shoichet BK, Taunton J
• Virtual discovery of melatonin receptor ligands to modulate circadian rhythms.
  Nature 2020 Stein RM, Kang HJ, McCorvy JD, Glatfelter GC, Jones AJ, Che T, Slocum S, Huang XP, Savych O, Moroz YS, Stauch B, Johansson LC, Cherezov V, Kenakin T, Irwin JJ, Shoichet BK, Roth BL, Dubocovich ML
• Docking Finds GPCR Ligands in Dark Chemical Matter.
  Journal of medicinal chemistry 2020 Ballante F, Rudling A, Zeifman A, Luttens A, Vo DD, Irwin JJ, Kihlberg J, Brea J, Loza MI, Carlsson J
• Ultra-large library docking for discovering new chemotypes.
  Nature 2019 Lyu J, Wang S, Balius TE, Singh I, Levit A, Moroz YS, O'Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK, Roth BL, Irwin JJ
• Predicted Biological Activity of Purchasable Chemical Space.
  Journal of chemical information and modeling 2017 Irwin JJ, Gaskins G, Sterling T, Mysinger MM, Keiser MJ
• Discovery of new GPCR ligands to illuminate new biology.
  Nature chemical biology 2017 Roth BL, Irwin JJ, Shoichet BK
• Identification of Novel Smoothened Ligands Using Structure-Based Docking.
  PloS one 2016 Lacroix C, Fish I, Torosyan H, Parathaman P, Irwin JJ, Shoichet BK, Angers S
• Docking Screens for Novel Ligands Conferring New Biology.
  Journal of medicinal chemistry 2016 Irwin JJ, Shoichet BK
• ZINC 15--Ligand Discovery for Everyone.
  Journal of chemical information and modeling 2015 Sterling T, Irwin JJ
• An Aggregation Advisor for Ligand Discovery.
  Journal of medicinal chemistry 2015 Irwin JJ, Duan D, Torosyan H, Doak AK, Ziebart KT, Sterling T, Tumanian G, Shoichet BK
• Erratum: Covalent docking of large libraries for the discovery of chemical probes.
  Nature chemical biology 2015 London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J
• Covalent docking of large libraries for the discovery of chemical probes.
  Nature chemical biology 2014 London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermancic P, Bonnet R, Shoichet BK, Taunton J
• Increasing chemical space coverage by combining empirical and computational fragment screens.
  ACS chemical biology 2014 Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G
• Novel compounds lowering the cellular isoform of the human prion protein in cultured human cells.
  Bioorganic & medicinal chemistry 2014 Silber BM, Gever JR, Rao S, Li Z, Renslo AR, Widjaja K, Wong C, Giles K, Freyman Y, Elepano M, Irwin JJ, Jacobson MP, Prusiner SB
• Covalent Docking of Large Libraries for the Discovery of Chemical Probes.
  Biophysical Journal 2014 Nir London, Rand M. Miller, John J. Irwin, Oliv Eidam, Lucie Gibold, Richard Bonnet, Brian K. Shoichet, Jack Taunton
• Ligand pose and orientational sampling in molecular docking.
  PloS one 2013 Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK
• Antiprion compounds that reduce PrP(Sc) levels in dividing and stationary-phase cells.
  Bioorganic & medicinal chemistry 2013 Silber BM, Gever JR, Li Z, Gallardo-Godoy A, Renslo AR, Widjaja K, Irwin JJ, Rao S, Jacobson MP, Ghaemmaghami S, Prusiner SB
• Structure-based discovery of antagonists of nuclear receptor LRH-1.
  The Journal of biological chemistry 2013 Benod C, Carlsson J, Uthayaruban R, Hwang P, Irwin JJ, Doak AK, Shoichet BK, Sablin EP, Fletterick RJ
• Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Geier EG, Schlessinger A, Fan H, Gable JE, Irwin JJ, Sali A, Giacomini KM
• Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.
  Journal of medicinal chemistry 2012 Mysinger MM, Carchia M, Irwin JJ, Shoichet BK
• Identifying mechanism-of-action targets for drugs and probes.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Gregori-Puigjané E, Setola V, Hert J, Crews BA, Irwin JJ, Lounkine E, Marnett L, Roth BL, Shoichet BK
• ZINC: a free tool to discover chemistry for biology.
  Journal of chemical information and modeling 2012 Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG
• Virtual ligand screening against comparative protein structure models.
  Methods in molecular biology (Clifton, N.J.) 2012 Fan H, Irwin JJ, Sali A
• Chemical informatics and target identification in a zebrafish phenotypic screen.
  Nature chemical biology 2011 Laggner C, Kokel D, Setola V, Tolia A, Lin H, Irwin JJ, Keiser MJ, Cheung CY, Minor DL, Roth BL, Peterson RT, Shoichet BK
• Statistical potential for modeling and ranking of protein-ligand interactions.
  Journal of chemical information and modeling 2011 Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A
• Ligand discovery from a dopamine D3 receptor homology model and crystal structure.
  Nature chemical biology 2011 Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, Shoichet BK
• Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Schlessinger A, Geier E, Fan H, Irwin JJ, Shoichet BK, Giacomini KM, Sali A
• The chemical basis of pharmacology.
  Biochemistry 2010 Keiser MJ, Irwin JJ, Shoichet BK
• The presynaptic component of the serotonergic system is required for clozapine's efficacy.
  Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology 2010 Yadav PN, Abbas AI, Farrell MS, Setola V, Sciaky N, Huang XP, Kroeze WK, Crawford LK, Piel DA, Keiser MJ, Irwin JJ, Shoichet BK, Deneris ES, Gingrich J, Beck SG, Roth BL
• Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors.
  Journal of medicinal chemistry 2010 Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin JJ, Shoichet BK
• Structure-based discovery of A2A adenosine receptor ligands.
  Journal of medicinal chemistry 2010 Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA
• A FRAMEWORK FOR EVALUATING REGIONAL-SCALE NUMERICAL PHOTOCHEMICAL MODELING SYSTEMS.
  Environmental fluid mechanics (Dordrecht, Netherlands : 2001) 2010 Dennis R, Fox T, Fuentes M, Gilliland A, Hanna S, Hogrefe C, Irwin J, Rao ST, Scheffe R, Schere K, Steyn D, Venkatram A
• Molecular docking screens using comparative models of proteins.
  Journal of chemical information and modeling 2009 Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A
• Predicting new molecular targets for known drugs.
  Nature 2009 Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB, Whaley R, Glennon RA, Hert J, Thomas KL, Edwards DD, Shoichet BK, Roth BL
• Automated docking screens: a feasibility study.
  Journal of medicinal chemistry 2009 Irwin JJ, Shoichet BK, Mysinger MM, Huang N, Colizzi F, Wassam P, Cao Y
• Docking and chemoinformatic screens for new ligands and targets.
  Current opinion in biotechnology 2009 Kolb P, Ferreira RS, Irwin JJ, Shoichet BK
• Staring off into chemical space.
  Nature chemical biology 2009 Irwin JJ
• Quantifying biogenic bias in screening libraries.
  Nature chemical biology 2009 Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK
• Structure-based discovery of beta2-adrenergic receptor ligands.
  Proceedings of the National Academy of Sciences of the United States of America 2009 Kolb P, Rosenbaum DM, Irwin JJ, Fung JJ, Kobilka BK, Shoichet BK
• Docking screens: right for the right reasons?
  Current topics in medicinal chemistry 2009 Kolb P, Irwin JJ
• ChemInform Abstract: Quantifying the Relationships among Drug Classes.
  ChemInform 2008 Jerome Hert, Michael J. Keiser, John J. Irwin, Tudor I. Oprea, Brian K. Shoichet
• A procedure for inter-comparing the skill of regional-scale air quality model simulations of daily maximum 8-h ozone concentrations.
  Atmospheric Environment 2008 John S. Irwin, Kevin Civerolo, Christian Hogrefe, Wyat Appel, Kristen Foley, Jenise Swall
• Using ZINC to acquire a virtual screening library.
  Current protocols in bioinformatics 2008 Irwin JJ
• Quantifying the relationships among drug classes.
  Journal of chemical information and modeling 2008 Hert J, Keiser MJ, Irwin JJ, Oprea TI, Shoichet BK
• Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase.
  Journal of medicinal chemistry 2008 Babaoglu K, Simeonov A, Irwin JJ, Nelson ME, Feng B, Thomas CJ, Cancian L, Costi MP, Maltby DA, Jadhav A, Inglese J, Austin CP, Shoichet BK
• Community benchmarks for virtual screening.
  Journal of computer-aided molecular design 2008 Irwin JJ
• Has the Performance of Regional-Scale Photochemical Modelling Systems Changed over the Past Decade?.
  2008 C. Hogrefe, J. -Y. Ku, G. Sistla, A. Gilliland, J. S. Irwin, P. S. Porter, E. Gégo, P. Kasibhatla, S. T. Rao
• Chemistry in cancer research: a vital partnership.
  Cancer research 2007 Sturla SJ, Irwin JJ, Loeppky RN, Mulvihill MJ, Searcey M
• Chemistry in cancer research: a vital partnership.
  ACS chemical biology 2007 Sturla SJ, Irwin JJ, Loeppky RN, Mulvihill MJ, Searcey M
• Relating protein pharmacology by ligand chemistry.
  Nature biotechnology 2007 Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK
• Evaluation of an Annual Simulation of Ozone and Fine Particulate Matter over the Continental United States – Which Temporal Features are Captured?.
  2007 Christian Hogrefe, J. M. Jones, A. Gilliland, P. Steven Porter, Edith Gégo, R. Gilliam, J. Swall, J. Irwin, S. T. Rao
• Objective Reduction of the Space-Time Domain Dimensionality for Evaluating Model Performance.
  2007 Edith Gégo, P. Steven Porter, Christian Hogrefe, R. Gilliam, A. Gilliland, J. Swall, J. Irwin, S. T. Rao
• Temporal Signatures of Observations and Model Outputs: Do Time Series Decomposition Methods Capture Relevant Time Scales?.
  2007 P. S. Porter, J. Swall, R. Gillian, E. L. Gego, Christian Hogrefe, A. Gilliland, J. S. Irwin, T. Rao
• Predicting substrates by docking high-energy intermediates to enzyme structures.
  Journal of the American Chemical Society 2006 Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK
• Benchmarking sets for molecular docking.
  Journal of medicinal chemistry 2006 Huang N, Shoichet BK, Irwin JJ
• An objective comparison of CMAQ and REMSAD performances.
  Atmospheric Environment 2006 Edith Gégo, P. Steven Porter, Christian Hogrefe, John S. Irwin
• Temporal features in observed and simulated meteorology and air quality over the Eastern United States.
  Atmospheric Environment 2006 C. Hogrefe, P.S. Porter, E. Gego, A. Gilliland, R. Gilliam, J. Swall, J. Irwin, S.T. Rao
• How good is your screening library?
  Current opinion in chemical biology 2006 Irwin JJ
• Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening.
  Journal of chemical information and modeling 2006 Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP
• Assessing the Comparability of Ammonium, Nitrate and Sulfate Concentrations Measured by Three Air Quality Monitoring Networks.
  Pure and Applied Geophysics 2005 Edith L Gego, P. Steven Porter, John S. Irwin, Christian Hogrefe, S. Trivikrama Rao
• Virtual screening against metalloenzymes for inhibitors and substrates.
  Biochemistry 2005 Irwin JJ, Raushel FM, Shoichet BK
• Here be dragons: docking and screening in an uncharted region of chemical space.
  Journal of biomolecular screening 2005 Brenk R, Irwin JJ, Shoichet BK
• ZINC — A Free Database of Commercially Available Compounds for Virtual Screening.
  ChemInform 2005 John J. Irwin, Brian K. Shoichet
• Examination of model predictions at different horizontal grid resolutions.
  Environmental Fluid Mechanics 2005 Edith Gego, Christian Hogrefe, George Kallos, Antigoni Voudouri, John S. Irwin, S. Trivikrama Rao
• Assessing the Comparability of Ammonium, Nitrate and Sulfate Concentrations Measured by Three Air Quality Monitoring Networks.
  2005 Edith L. Gego, P. Steven Porter, John S. Irwin, Christian Hogrefe, S. Trivikrama Rao
• ZINC--a free database of commercially available compounds for virtual screening.
  Journal of chemical information and modeling 2005 Irwin JJ, Shoichet BK
• Comparison of the Space-Time Signatures of Air Quality Data From Different Monitoring Networks.
  2004 Edith L. Gego, Christian Hogrefe, P. Steven Porter, John S. Irwin, S. Trivikrama Rao
• A molecular docking strategy identifies Eosin B as a non-active site inhibitor of protozoal bifunctional thymidylate synthase-dihydrofolate reductase.
  The Journal of biological chemistry 2003 Atreya CE, Johnson EF, Irwin JJ, Dow A, Massimine KM, Coppens I, Stempliuk V, Beverley S, Joiner KA, Shoichet BK, Anderson KS
• Lead discovery using molecular docking.
  Current opinion in chemical biology 2002 Shoichet BK, McGovern SL, Wei B, Irwin JJ