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Tuning Potential Functions to Host-Guest Binding Data.
Setiadi J, Boothroyd S, Slochower DR, Dotson DL, Thompson MW, Wagner JR, Wang LP, Gilson MK. Setiadi J, et al. Among authors: wagner jr. J Chem Theory Comput. 2024 Jan 9;20(1):239-252. doi: 10.1021/acs.jctc.3c01050. Epub 2023 Dec 26. J Chem Theory Comput. 2024. PMID: 38147689
POVME 3.0: Software for Mapping Binding Pocket Flexibility.
Wagner JR, Sørensen J, Hensley N, Wong C, Zhu C, Perison T, Amaro RE. Wagner JR, et al. J Chem Theory Comput. 2017 Sep 12;13(9):4584-4592. doi: 10.1021/acs.jctc.7b00500. Epub 2017 Aug 30. J Chem Theory Comput. 2017. PMID: 28800393 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. 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.
Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs.
Smith DGA, Lolinco AT, Glick ZL, Lee J, Alenaizan A, Barnes TA, Borca CH, Di Remigio R, Dotson DL, Ehlert S, Heide AG, Herbst MF, Hermann J, Hicks CB, Horton JT, Hurtado AG, Kraus P, Kruse H, Lee SJR, Misiewicz JP, Naden LN, Ramezanghorbani F, Scheurer M, Schriber JB, Simmonett AC, Steinmetzer J, Wagner JR, Ward L, Welborn M, Altarawy D, Anwar J, Chodera JD, Dreuw A, Kulik HJ, Liu F, Martínez TJ, Matthews DA, Schaefer HF 3rd, Šponer J, Turney JM, Wang LP, De Silva N, King RA, Stanton JF, Gordon MS, Windus TL, Sherrill CD, Burns LA. Smith DGA, et al. Among authors: wagner jr. J Chem Phys. 2021 Nov 28;155(20):204801. doi: 10.1063/5.0059356. J Chem Phys. 2021. PMID: 34852489 Free PMC article.
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale.
Horton JT, Boothroyd S, Wagner J, Mitchell JA, Gokey T, Dotson DL, Behara PK, Ramaswamy VK, Mackey M, Chodera JD, Anwar J, Mobley DL, Cole DJ. Horton JT, et al. J Chem Inf Model. 2022 Nov 28;62(22):5622-5633. doi: 10.1021/acs.jcim.2c01153. Epub 2022 Nov 9. J Chem Inf Model. 2022. PMID: 36351167 Free PMC article.
Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field.
D'Amore L, Hahn DF, Dotson DL, Horton JT, Anwar J, Craig I, Fox T, Gobbi A, Lakkaraju SK, Lucas X, Meier K, Mobley DL, Narayanan A, Schindler CEM, Swope WC, In 't Veld PJ, Wagner J, Xue B, Tresadern G. D'Amore L, et al. J Chem Inf Model. 2022 Dec 12;62(23):6094-6104. doi: 10.1021/acs.jcim.2c01185. Epub 2022 Nov 26. J Chem Inf Model. 2022. PMID: 36433835 Free PMC article.
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field.
Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang LP, Cole DJ, Gilson MK, Chodera JD, Bayly CI, Shirts MR, Mobley DL. Boothroyd S, et al. Among authors: wagner jr. J Chem Theory Comput. 2023 Jun 13;19(11):3251-3275. doi: 10.1021/acs.jctc.3c00039. Epub 2023 May 11. J Chem Theory Comput. 2023. PMID: 37167319 Free PMC article.
1,389 results