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Page 1
Gaussian-mixture umbrella sampling.
Maragakis P, van der Vaart A, Karplus M. Maragakis P, et al. Among authors: van der vaart a. J Phys Chem B. 2009 Apr 9;113(14):4664-73. doi: 10.1021/jp808381s. J Phys Chem B. 2009. PMID: 19284746 Free PMC article.
Systematic assessment of the flexibility of uracil damaged DNA.
Orndorff PB, van der Vaart A. Orndorff PB, et al. Among authors: van der vaart a. J Biomol Struct Dyn. 2024 May;42(8):3958-3968. doi: 10.1080/07391102.2023.2217683. Epub 2023 Jun 1. J Biomol Struct Dyn. 2024. PMID: 37261803
Uracil-DNA glycosylase efficiency is modulated by substrate rigidity.
Orndorff PB, Poddar S, Owens AM, Kumari N, Ugaz BT, Amin S, Van Horn WD, van der Vaart A, Levitus M. Orndorff PB, et al. Among authors: van der vaart a, van horn wd. Sci Rep. 2023 Mar 8;13(1):3915. doi: 10.1038/s41598-023-30620-0. Sci Rep. 2023. PMID: 36890276 Free PMC article.
Protein structural transitions and their functional role.
Karplus M, Gao YQ, Ma J, van der Vaart A, Yang W. Karplus M, et al. Among authors: van der vaart a. Philos Trans A Math Phys Eng Sci. 2005 Feb 15;363(1827):331-55; discussion 355-6. doi: 10.1098/rsta.2004.1496. Philos Trans A Math Phys Eng Sci. 2005. PMID: 15664887 Review.
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: van der vaart a. 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.
149 results