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End-to-end differentiable construction of molecular mechanics force fields.
Wang Y, Fass J, Kaminow B, Herr JE, Rufa D, Zhang I, Pulido I, Henry M, Bruce Macdonald HE, Takaba K, Chodera JD. Wang Y, et al. Among authors: zhang i. Chem Sci. 2022 Sep 8;13(41):12016-12033. doi: 10.1039/d2sc02739a. eCollection 2022 Oct 26. Chem Sci. 2022. PMID: 36349096 Free PMC article.
Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex.
Zhang I, Rufa DA, Pulido I, Henry MM, Rosen LE, Hauser K, Singh S, Chodera JD. Zhang I, et al. bioRxiv [Preprint]. 2023 Jun 21:2023.03.07.530278. doi: 10.1101/2023.03.07.530278. bioRxiv. 2023. Update in: J Chem Theory Comput. 2023 Aug 8;19(15):4863-4882. doi: 10.1021/acs.jctc.3c00333 PMID: 36945557 Free PMC article. Updated. Preprint.
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.
Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, Rodriguez-Guerra J, Simmonett AC, Singh S, Swails J, Turner P, Wang Y, Zhang I, Chodera JD, Fabritiis G, Markland TE. Eastman P, et al. Among authors: zhang i. ArXiv [Preprint]. 2023 Nov 29:arXiv:2310.03121v2. ArXiv. 2023. Update in: J Phys Chem B. 2024 Jan 11;128(1):109-116. doi: 10.1021/acs.jpcb.3c06662 PMID: 37986730 Free PMC article. Updated. Preprint.
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.
Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, Rodriguez-Guerra J, Simmonett AC, Singh S, Swails J, Turner P, Wang Y, Zhang I, Chodera JD, De Fabritiis G, Markland TE. Eastman P, et al. Among authors: zhang i. J Phys Chem B. 2024 Jan 11;128(1):109-116. doi: 10.1021/acs.jpcb.3c06662. Epub 2023 Dec 28. J Phys Chem B. 2024. PMID: 38154096 Free PMC article.
Ecological dynamics explain modular denitrification in the ocean.
Sun X, Buchanan PJ, Zhang IH, San Roman M, Babbin AR, Zakem EJ. Sun X, et al. Among authors: zhang ih. Proc Natl Acad Sci U S A. 2024 Dec 24;121(52):e2417421121. doi: 10.1073/pnas.2417421121. Epub 2024 Dec 18. Proc Natl Acad Sci U S A. 2024. PMID: 39693347 Free PMC article.
235 results