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Sharing Data from Molecular Simulations.
Abraham M, Apostolov R, Barnoud J, Bauer P, Blau C, Bonvin AMJJ, Chavent M, Chodera J, Čondić-Jurkić K, Delemotte L, Grubmüller H, Howard RJ, Jordan EJ, Lindahl E, Ollila OHS, Selent J, Smith DGA, Stansfeld PJ, Tiemann JKS, Trellet M, Woods C, Zhmurov A. Abraham M, et al. Among authors: chodera j. J Chem Inf Model. 2019 Oct 28;59(10):4093-4099. doi: 10.1021/acs.jcim.9b00665. Epub 2019 Oct 11. J Chem Inf Model. 2019. PMID: 31525920
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.
Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS. Eastman P, et al. Among authors: chodera jd. PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. doi: 10.1371/journal.pcbi.1005659. eCollection 2017 Jul. PLoS Comput Biol. 2017. PMID: 28746339 Free PMC article.
Is Structure-Based Drug Design Ready for Selectivity Optimization?
Albanese SK, Chodera JD, Volkamer A, Keng S, Abel R, Wang L. Albanese SK, et al. J Chem Inf Model. 2020 Dec 28;60(12):6211-6227. doi: 10.1021/acs.jcim.0c00815. Epub 2020 Oct 29. J Chem Inf Model. 2020. PMID: 33119284 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: chodera jd. 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. Among authors: chodera jd. 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.
136 results