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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: rizzi a. 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. 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.
Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia.
Minuesa G, Albanese SK, Xie W, Kazansky Y, Worroll D, Chow A, Schurer A, Park SM, Rotsides CZ, Taggart J, Rizzi A, Naden LN, Chou T, Gourkanti S, Cappel D, Passarelli MC, Fairchild L, Adura C, Glickman JF, Schulman J, Famulare C, Patel M, Eibl JK, Ross GM, Bhattacharya S, Tan DS, Leslie CS, Beuming T, Patel DJ, Goldgur Y, Chodera JD, Kharas MG. Minuesa G, et al. Among authors: rizzi a. Nat Commun. 2019 Jun 19;10(1):2691. doi: 10.1038/s41467-019-10523-3. Nat Commun. 2019. PMID: 31217428 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. 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.
Best Practices for Alchemical Free Energy Calculations [Article v1.0].
Mey ASJS, Allen BK, Macdonald HEB, Chodera JD, Hahn DF, Kuhn M, Michel J, Mobley DL, Naden LN, Prasad S, Rizzi A, Scheen J, Shirts MR, Tresadern G, Xu H. Mey ASJS, et al. Among authors: rizzi a. Living J Comput Mol Sci. 2020;2(1):18378. doi: 10.33011/livecoms.2.1.18378. Living J Comput Mol Sci. 2020. PMID: 34458687 Free PMC article.
Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.
Qiu Y, Smith DGA, Boothroyd S, Jang H, Hahn DF, Wagner J, Bannan CC, Gokey T, Lim VT, Stern CD, Rizzi A, Tjanaka B, Tresadern G, Lucas X, Shirts MR, Gilson MK, Chodera JD, Bayly CI, Mobley DL, Wang LP. Qiu Y, et al. Among authors: rizzi a. J Chem Theory Comput. 2021 Oct 12;17(10):6262-6280. doi: 10.1021/acs.jctc.1c00571. Epub 2021 Sep 22. J Chem Theory Comput. 2021. PMID: 34551262 Free PMC article.
992 results