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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: chodera jd. 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.
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.
Escaping Atom Types in Force Fields Using Direct Chemical Perception.
Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK. Mobley DL, et al. Among authors: chodera jd. J Chem Theory Comput. 2018 Nov 13;14(11):6076-6092. doi: 10.1021/acs.jctc.8b00640. Epub 2018 Oct 30. J Chem Theory Comput. 2018. PMID: 30351006 Free PMC article.
Overview of the SAMPL6 host-guest binding affinity prediction challenge.
Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Rizzi A, et al. Among authors: chodera jd. J Comput Aided Mol Des. 2018 Oct;32(10):937-963. doi: 10.1007/s10822-018-0170-6. Epub 2018 Nov 10. J Comput Aided Mol Des. 2018. PMID: 30415285 Free PMC article.
Toward Learned Chemical Perception of Force Field Typing Rules.
Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Zanette C, et al. Among authors: chodera jd. J Chem Theory Comput. 2019 Jan 8;15(1):402-423. doi: 10.1021/acs.jctc.8b00821. Epub 2018 Dec 24. J Chem Theory Comput. 2019. PMID: 30512951 Free PMC article.
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.
Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, Mobley DL, Chodera JD. Rizzi A, et al. Among authors: chodera jd. J Comput Aided Mol Des. 2020 May;34(5):601-633. doi: 10.1007/s10822-020-00290-5. Epub 2020 Jan 27. J Comput Aided Mol Des. 2020. PMID: 31984465 Free PMC article.
134 results