Transition path sampling: throwing ropes over rough mountain passes, in the dark.

By Peter G. Bolhuis, D. Chandler, Christoph Dellago, P. Geissler. Annual review of physical chemistry (Print), 2002

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Experimental accuracy in protein structure refinement via molecular dynamics simulations (2018, background): “While many types of conformational transitions have been studied via many different methods (45, 46), we chose the iterative sampling protocol based on unbiased simulations to study the refinement transition without having to make any pre-sumptions about the pathway(s) or suitable progress…”
Elaborating transition interface sampling methods (2004, positive): “Instead, it is suﬃcient but necessary that this function is able to characterize the basins of attraction of the stable states [13].”
Allostery and cooperativity revisited (2008, background): “…in ligand binding processes is not surprising, given that the residual configurational entropy in a small folded protein, such as BPTI, which is made up of 58 residues, has been estimated to be 602 kcal/mol at 300 K by normal mode simulations with quantum corrections (Brooks and Karplus 1983).”
Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space. (2013, methodology): “These include even the comparatively sophisticated techniques that have now been developed to improve the sampling of rare events, such as milestoning (65), transition path sampling (66), and metadynamics (67).”