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CHARMM: the biomolecular simulation program.
Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. Brooks BR, et al. Among authors: hodoscek m. J Comput Chem. 2009 Jul 30;30(10):1545-614. doi: 10.1002/jcc.21287. J Comput Chem. 2009. PMID: 19444816 Free PMC article. Review.
Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms.
Woodcock HL, Hodoscek M, Brooks BR. Woodcock HL, et al. Among authors: hodoscek m. J Phys Chem A. 2007 Jul 5;111(26):5720-8. doi: 10.1021/jp0714217. Epub 2007 Jun 8. J Phys Chem A. 2007. PMID: 17555303
Full reaction paths were independently mapped with RPATh and NEB methods and showed good agreement with the final transition state from the RPATh+RESD "gold standard" and previous high-level QM/MM transition states (Woodcock, H. L.; Hodoscek, M.; Gilbert, T. B.; Gil …
Full reaction paths were independently mapped with RPATh and NEB methods and showed good agreement with the final transition state from the …
CHARMMing: a new, flexible web portal for CHARMM.
Miller BT, Singh RP, Klauda JB, Hodoscek M, Brooks BR, Woodcock HL 3rd. Miller BT, et al. Among authors: hodoscek m. J Chem Inf Model. 2008 Sep;48(9):1920-9. doi: 10.1021/ci800133b. Epub 2008 Aug 13. J Chem Inf Model. 2008. PMID: 18698840 Free PMC article.
MSCALE: A General Utility for Multiscale Modeling.
Woodcock HL, Miller BT, Hodoscek M, Okur A, Larkin JD, Ponder JW, Brooks BR. Woodcock HL, et al. Among authors: hodoscek m. J Chem Theory Comput. 2011 Apr 12;7(4):1208-1219. doi: 10.1021/ct100738h. J Chem Theory Comput. 2011. PMID: 21691425 Free PMC article.
61 results