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CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding.
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, Hillisch A, Hogner A, Irwin JJ, Jansen JM, Kuhn D, Leach AR, Lee AA, Lessel U, Morgan MR, Moult J, Muegge I, Oprea TI, Perry BG, Riley P, Rousseaux SAL, Saikatendu KS, Santhakumar V, Schapira M, Scholten C, Todd MH, Vedadi M, Volkamer A, Willson TM. Ackloo S, et al. Among authors: amaro re. Nat Rev Chem. 2022 Apr;6(4):287-295. doi: 10.1038/s41570-022-00363-z. Epub 2022 Feb 15. Nat Rev Chem. 2022. PMID: 35783295 Free PMC article.
Computational chemistry and drug discovery: a call to action.
Jansen JM, Amaro RE, Cornell W, Tseng YJ, Walters WP. Jansen JM, et al. Among authors: amaro re. Future Med Chem. 2012 Oct;4(15):1893-6. doi: 10.4155/fmc.12.137. Future Med Chem. 2012. PMID: 23088271 No abstract available.
Ensemble Docking in Drug Discovery.
Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. Amaro RE, et al. Biophys J. 2018 May 22;114(10):2271-2278. doi: 10.1016/j.bpj.2018.02.038. Epub 2018 Mar 30. Biophys J. 2018. PMID: 29606412 Free PMC article. Review.
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Parks CD, Gaieb Z, Chiu M, Yang H, Shao C, Walters WP, Jansen JM, McGaughey G, Lewis RA, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK. Parks CD, et al. Among authors: amaro re. J Comput Aided Mol Des. 2020 Feb;34(2):99-119. doi: 10.1007/s10822-020-00289-y. Epub 2020 Jan 23. J Comput Aided Mol Des. 2020. PMID: 31974851 Free PMC article.
A critical overview of computational approaches employed for COVID-19 drug discovery.
Muratov EN , Amaro R , Andrade CH , Brown N , Ekins S , Fourches D , Isayev O , Kozakov D , Medina-Franco JL , Merz KM , Oprea TI , Poroikov V , Schneider G , Todd MH , Varnek A , Winkler DA , Zakharov AV , Cherkasov A , Tropsha A . Muratov EN , et al. Chem Soc Rev. 2021 Aug 21;50(16):9121-9151. doi: 10.1039/d0cs01065k. Epub 2021 Jul 2. Chem Soc Rev. 2021. PMID: 34212944 Free PMC article. Review.
218 results