Christian R. Schwantes; Diwakar Shukla; Vijay S. Pande
2016-04-01 (print)
Biophysical Journal (Biophys. J.). 110, 8, 1716-1719. doi:10.1016/j.bpj.2016.03.026
They find an intermediate in 2011-larsen-folding NuG2 trajectories that is a register shift that was missed before tICA+MSM.
Robert McGibbon
2014-05-01 (online)
K. Lindorff-Larsen; S. Piana; R. O. Dror; D. E. Shaw
2011-10-27 (online) – 2011-10-28 (print)
Science (Science). 334, 6055, 517-520. doi:10.1126/science.1208351
The authors simulated folding trajectories for 12 small proteins. The simulations were between 100 us and 1 ms. This paper was a considerable advance for the field, and more or less closed the book on molecular dynamics for folding.
simulations
D. E. Shaw; P. Maragakis; K. Lindorff-Larsen; S. Piana; R. O. Dror; M. P. Eastwood; J. A. Bank; J. M. Jumper; J. K. Salmon; Y. Shan; W. Wriggers
2010-10-14 (online) – 2010-10-15 (print)
Science (Science). 330, 6002, 341-346. doi:10.1126/science.1187409
Simulation of fip35 ww domain: 2x 100 us. Note this was at 400K so unfolding could be observed.
Simulation of bpti: 1ms. Note this was done with tip4p for reasons.
simulations
Frank Noé; Dieter Krachtus; Jeremy C. Smith; Stefan Fischer
2006-05-01 (print)
Journal of Chemical Theory and Computation (J. Chem. Theory Comput.). 2, 3, 840-857. doi:10.1021/ct050162r
conformational-change
S. Fischer; B. Windshugel; D. Horak; K. C. Holmes; J. C. Smith
2005-04-29 (online) – 2005-05-10 (print)
Proceedings of the National Academy of Sciences (Proc. Natl. Acad. Sci. U.S.A.). 102, 19, 6873-6878. doi:10.1073/pnas.0408784102
conformational-change