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Page 1
Ultra-large library docking for discovering new chemotypes.
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. Lyu J, et al. Nature. 2019 Feb;566(7743):224-229. doi: 10.1038/s41586-019-0917-9. Epub 2019 Feb 6. Nature. 2019. PMID: 30728502 Free PMC article.
The Recognition of Identical Ligands by Unrelated Proteins.
Barelier S, Sterling T, O'Meara MJ, Shoichet BK. Barelier S, et al. ACS Chem Biol. 2015 Dec 18;10(12):2772-84. doi: 10.1021/acschembio.5b00683. Epub 2015 Oct 12. ACS Chem Biol. 2015. PMID: 26421501 Free PMC article.
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS,… See abstract for full author list ➔ Gordon DE, et al. Nature. 2020 Jul;583(7816):459-468. doi: 10.1038/s41586-020-2286-9. Epub 2020 Apr 30. Nature. 2020. PMID: 32353859 Free PMC article.
Property-Unmatched Decoys in Docking Benchmarks.
Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ. Stein RM, et al. J Chem Inf Model. 2021 Feb 22;61(2):699-714. doi: 10.1021/acs.jcim.0c00598. Epub 2021 Jan 25. J Chem Inf Model. 2021. PMID: 33494610 Free PMC article.
Drug-induced phospholipidosis confounds drug repurposing for SARS-CoV-2.
Tummino TA, Rezelj VV, Fischer B, Fischer A, O'Meara MJ, Monel B, Vallet T, White KM, Zhang Z, Alon A, Schadt H, O'Donnell HR, Lyu J, Rosales R, McGovern BL, Rathnasinghe R, Jangra S, Schotsaert M, Galarneau JR, Krogan NJ, Urban L, Shokat KM, Kruse AC, García-Sastre A, Schwartz O, Moretti F, Vignuzzi M, Pognan F, Shoichet BK. Tummino TA, et al. Science. 2021 Jul 30;373(6554):541-547. doi: 10.1126/science.abi4708. Epub 2021 Jun 22. Science. 2021. PMID: 34326236 Free PMC article.
Structures of the σ2 receptor enable docking for bioactive ligand discovery.
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. Alon A, et al. Nature. 2021 Dec;600(7890):759-764. doi: 10.1038/s41586-021-04175-x. Epub 2021 Dec 8. Nature. 2021. PMID: 34880501 Free PMC article.
Prediction of enzymatic pathways by integrative pathway mapping.
Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A. Calhoun S, et al. Elife. 2018 Jan 29;7:e31097. doi: 10.7554/eLife.31097. Elife. 2018. PMID: 29377793 Free PMC article.
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing.
Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Wankowicz SA, Bohn M, Sharp PP, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Rosenberg OS, Verba KA, Agard D, Ott M, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Ashworth A, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. Gordon DE, et al. bioRxiv [Preprint]. 2020 Mar 27:2020.03.22.002386. doi: 10.1101/2020.03.22.002386. bioRxiv. 2020. Update in: Nature. 2020 Jul;583(7816):459-468. doi: 10.1038/s41586-020-2286-9 PMID: 32511329 Free PMC article. Updated. Preprint.
Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets.
Fu C, Zhang X, Veri AO, Iyer KR, Lash E, Xue A, Yan H, Revie NM, Wong C, Lin ZY, Polvi EJ, Liston SD, VanderSluis B, Hou J, Yashiroda Y, Gingras AC, Boone C, O'Meara TR, O'Meara MJ, Noble S, Robbins N, Myers CL, Cowen LE. Fu C, et al. Nat Commun. 2021 Nov 11;12(1):6497. doi: 10.1038/s41467-021-26850-3. Nat Commun. 2021. PMID: 34764269 Free PMC article.
48 results