top of page
Publications

Publications detailing some of the ORRxD methodology, hit discovery and lead optimization work listed below:

  1. W. EVANGELISTA, R. L. WEIR, S. R. ELLINGSON, J. B. HARRIS, K. KAPOOR, J. C. SMITH, AND J. BAUDRY.  Ensemble-based docking: from hit discovery to metabolism and toxicity predictions. Bioorganic & Medicinal Chemistry.  24(20) 4928-4935 (2016).

  2. Z.S. XIAO, D. RICCARDI, H.A. VELAZQUEZ, A.L. CHIN, C.R. YATES, J.D. CARRICK, J.C. SMITH, J. BAUDRY, AND L.D. QUARLES.  Computationally Identified Novel Chemical Compounds that Antagonize FGF-23.  Science Signaling. 9 (455) ra113 (2016).

  3. N. ABDALI, J.M. PARKS, K. HAYNES, J.L. CHANEY, A.T. GREEN, D. WOLLOSCHECK, J.K. WALKER, V. RYBENKOV, J.Y. BAUDRY, J.C. SMITH, H. ZGURSKAYA.  Reviving antibiotics: efflux pump inhibitors that interact with AcrA, a membrane fusion protein of the AcrAB-TolC multidrug efflux pump.  ACS Infectious Diseases.    3 (1), 89–98 (2017)

  4. K M HAYNES, N ABDALI, V JHAWAR, HI ZGURSKAYA, JM PARKS, AT GREEN, J BAUDRY, V V RYBENKOV, J C SMITH, J K WALKER. Identification and Structure–Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli Journal of Medicinal Chemistry 60(14) 6205-6219 (2017).

  5. H. A. VELAZQUEZ, D. RICCARDI, Z. XIAO, D. QUARLES, C. R. YATES, J. BAUDRY & J. C. SMITH. Ensemble Docking to Difficult Targets in Early-Stage Drug Discovery: Methodology and Application to Fibroblast Growth Factor 23. Chemical Biology & Drug Design. 91.2 (2018): 491-504.

  6. Z. XIAO, J. BAUDRY, L. CAO, J. HUANG, C. R. YATES, J. C. SMITH & L. D. QUARLES.  Polycystin-1 interacts with TAZ to stimulate osteoblastogenesis and inhibit adipogenesis. Journal of Clinical Investigation. 128 (1), 157-174 (2018)

  7. M. PI, K. KAPOOR, R. YE, J. C. SMITH, J. BAUDRY AND L. D. QUARLES. GPCR6A is a Molecular Target for the Natural Products Gallate and EGCG in Green Tea. Molecular Nutrition and Food Research. 62 (8), 1700770 (2018)

  8. R. E. AMARO, J. BAUDRY, J. CHODERA, Ö. DEMIR, J. A. MCCAMMON, Y. MIAO AND J. C. SMITH. Ensemble Docking in Drug Discovery. Biophysical Journal. 114 (10) 2271-2278 (2018)

  9. M. PI, K. KAPOOR, R. YE, D.-J. HWANG, D. D. MILLER, J. C. SMITH, J. BAUDRY  & L. D. QUARLES. Computationally Identified Novel Agonists for GPRC6A. PLoS ONE.  13 (4), e0195980 (2018)

  10. Z. M. DARZYNKIEWICZ, A. T. GREEN, N. ABDALI, A. HAZEL, R. L. FULTON, J. KIMBALL, Z. GRYCZYNSKI, J.C. GUMBART, J.M. PARKS, J.C. SMITH AND H.I. ZGURSKAYA. Identification of Binding Sites for Efflux Pump Inhibitors of the Escherichia coli AcrAB-TolC component AcrA. Biophysical Journal. 116(4):648-658 (2019)

  11. W. EVANGELISTA,  S. ELLINGSON,  J.C. SMITH, J.Y. BAUDRY, Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations Are Needed to Reproduce Known Ligand Binding?  Journal of Physical Chemistry 123 (25), 5189-5195 (2019)

  12. A.T. GREEN, MONIRUZZAMAN M, COOPER CJ, WALKER JK, SMITH JC, PARKS JM, AND ZGURSKAYA ZI. Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold. Biochimica et Biophysica Acta – General Subjects. 1864, 6, 129546, (2020)

  13. J. M. PARKS and J.C. SMITH. How to discover antiviral compounds quickly. New England Journal of Medicine, 382;23 2262-2264 (2020)

  14. M.D. SMITH and J.C.SMITH. Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface ChemRXiv. https://doi.org/10.26434/chemrxiv.11871402.v3

  15. S LEGRAND M THAVAPPIRAGASAM J LARKIN L SOLIS-VASQUEZ O HERNANDEZ, A SCHEINBERG J V. VERMAAS, D POOLE A KOCH F. TILLACK R AGARWAL D SANTOS-MARTINS S FORLI J C. SMITH, A SEDOVA GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB ’20), September 21–24, 2020, Virtual Event, USA. ACM, New York, NY, USA, 10 pages. https://doi.org/10.1145/3388440.3412472

  16. R. AGARWAL, B. A. BENSING, D. MI, J. BAUDRY, T. M. IVERSON, J. C. SMITH. Structure based virtual screening identifies small molecule effectors for the sialoglycan binding protein Hsa. Biochemical Journal, 477.19: 3695-3707 (2020)

  17. A. ACHARYA, R. AGARWAL, M. BAKER , J. BAUDRY, D. BHOWMIK, S. BOEHM, K. G. BYLER, S.Y. CHEN, L. COATES, C.J. COOPER, O. DEMERDASH, I. DAIDONE, J.D. EBLEN, S. ELLINGSON, S. FORLI J. GLASER, J. C. GUMBART, J. GUNNELS, O. HERNANDEZ, S. IRLE, D.W. KNELLER, A. KOVALEVSKY, J. LARKIN, T.J. LAWRENCE, S. LEGRAND, S.-H. LIU, J.C. MITCHELL, G. PARK, J.M. PARKS, A. PAVLOVA, L. PETRIDIS, D. POOLE, L. POUCHARD, A. RAMANATHAN, D. ROGERS, D. SANTOS-MARTINS A. SCHEINBERG, A. SEDOVA, S. SHEN, J.C. SMITH, M.D. SMITH, C. SOTO, A. TSARIS, M. THAVAPPIRAGASAM, A.F. TILLACK, J.V. VERMAAS, V.Q. VUONG J.YIN,  S. YOO9 M. ZAHRAN , L. ZANETTI-POLZI Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 Journal of Chemical Information and Modeling. 60(12) 5832-5852 (2020)

  18. J. V. VERMAAS, A. SEDOVA, M. B. BAKER, S.  BOEHM, D. M. ROGERS, J. LARKIN, J. GLASER, M. D. SMITH, O. HERNANDEZ, J C. SMITH. Supercomputing Pipelines Search for Therapeutics Against COVID-19 IEEE Computing in Science & Engineering, In Press. (2020)

  19. S LEGRAND M THAVAPPIRAGASAM J LARKIN L SOLIS-VASQUEZ O HERNANDEZ, A SCHEINBERG J V. VERMAAS, D POOLE A KOCH F. TILLACK R AGARWAL D SANTOS-MARTINS S FORLI J C. SMITH, A SEDOVA GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB ’20), September 21–24, 2020, Virtual Event, USA. ACM, New York, NY, USA, 10 pages. https://doi.org/10.1145/3388440.3412472

bottom of page