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pyCHARMM: Embedding CHARMM Functionality in a Python Framework.
Buckner J, Liu X, Chakravorty A, Wu Y, Cervantes LF, Lai TT, Brooks CL 3rd. Buckner J, et al. J Chem Theory Comput. 2023 Jun 27;19(12):3752-3762. doi: 10.1021/acs.jctc.3c00364. Epub 2023 Jun 2. J Chem Theory Comput. 2023. PMID: 37267404 Free PMC article.
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL 3rd, MacKerell AD Jr, Klauda JB, Im W. Lee J, et al. Among authors: buckner j. J Chem Theory Comput. 2016 Jan 12;12(1):405-13. doi: 10.1021/acs.jctc.5b00935. Epub 2015 Dec 3. J Chem Theory Comput. 2016. PMID: 26631602 Free PMC article.
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.
Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE 2nd, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, Käser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD Jr, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, Töpfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL 3rd, Brooks BR, Karplus M. Hwang W, et al. Among authors: buckner j. J Phys Chem B. 2024 Oct 17;128(41):9976-10042. doi: 10.1021/acs.jpcb.4c04100. Epub 2024 Sep 20. J Phys Chem B. 2024. PMID: 39303207 Free PMC article. Review.
The gputools package enables GPU computing in R.
Buckner J, Wilson J, Seligman M, Athey B, Watson S, Meng F. Buckner J, et al. Bioinformatics. 2010 Jan 1;26(1):134-5. doi: 10.1093/bioinformatics/btp608. Epub 2009 Oct 22. Bioinformatics. 2010. PMID: 19850754 Free PMC article.
Systemic inflammation and lymphocyte activation precede rheumatoid arthritis.
He Z, Glass MC, Venkatesan P, Feser ML, Lazaro L, Okada LY, Tran NTT, He YD, Rachid Zaim S, Bennett CE, Ravisankar P, Dornisch EM, Arishi NA, Asamoah AG, Barzideh S, Becker LA, Bemis EA, Buckner JH, Collora CE, Criley MAL, Demoruelle MK, Fleischer CL, Garber J, Genge PC, Gong Q, Graybuck LT, Gustafson CE, Hattel BC, Hernandez V, Heubeck AT, Kawelo EK, Krishnan U, Kuan EL, Kuhn KA, LaFrance CM, Lee KJ, Li R, Lord C, Mettey RR, Moss L, Musgrove B, Nguyen K, Ochoa A, Parthasarathy V, Pebworth MP, Pedrick C, Peng T, Phalen CG, Reading J, Roll CR, Seifert JA, Siedschlag MD, Speake C, Striebich CC, Stuckey TJ, Swanson EG, Takada H, Thai T, Thomson ZJ, Trieu N, Tsaltskan V, Wang W, Weiss MDA, Westermann A, Zhang F, Boyle DL, Goldrath AW, Bumol TF, Li XJ, Holers VM, Skene PJ, Savage AK, Firestein GS, Deane KD, Torgerson TR, Gillespie MA. He Z, et al. Among authors: buckner jh. bioRxiv [Preprint]. 2024 Nov 12:2024.10.25.620344. doi: 10.1101/2024.10.25.620344. bioRxiv. 2024. PMID: 39554042 Free PMC article. Preprint.
Identification of a novel PDC-E2 epitope in primary biliary cholangitis: Application for engineered Treg therapy.
Tewari R, Yang SJ, McClain ED, Hu A, Mortensen E, DeSchmidt A, Chen J, Kancharla A, Singh AK, James EA, Burman BE, Siddique A, Rawlings DJ, Patel C, Cerosaletti K, Buckner JH. Tewari R, et al. Among authors: buckner jh. J Autoimmun. 2024 Oct 29;149:103327. doi: 10.1016/j.jaut.2024.103327. Online ahead of print. J Autoimmun. 2024. PMID: 39476446
761 results