What are some of the applications for these techniques?

MSMs and adaptive sampling have been used to study protein folding (1-8), functional dynamics (8-11), ligand-binding (11-14), and protein-protein interactions (15).

  1. Jayachandran G, Vishal V, & Pande VS (2006) Using massively parallel simulation and Markovian models to study protein folding: Examining the dynamics of the villin headpiece. Journal of Chemical Physics 124:164902.
  2. Bowman GR, Beauchamp KA, Boxer G, & Pande VS (2009) Progress and challenges in the automated construction of Markov state models for full protein systems. Journal of Chemical Physics 131(12):124101.
  3. Noe F, Schutte C, Vanden-Eijnden E, Reich L, & Weikl TR (2009) Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proceedings of the National Academy of Sciences of the USA 106(45):19011-19016.
  4. Bowman GR & Pande VS (2010) Protein folded states are kinetic hubs. Proceedings of the National Academy of Sciences of the USA 107(24):10890-10895.
  5. Beauchamp KA, Ensign DL, Das R, & Pande VS (2011) Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments. Proc Natl Acad Sci USA 108:12734-12739.
  6. Bowman GR, Voelz VA, & Pande VS (2011) Atomistic folding simulations of the five-helix bundle protein (6-85). Journal of the American Chemical Society 133(4):664-667.
  7. Voelz VA et al. (2012) Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. Journal of the American Chemical Society 134(30):12565-12577.
  8. Lane TJ, Bowman GR, Beauchamp K, Voelz VA, & Pande VS (2011) Markov state model reveals folding and functional dynamics in ultra-long MD trajectories. Journal of the American Chemical Society 133(45):18413-18419.
  9. Yang S, Banavali NK, & Roux B (2009) Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories. Proc Natl Acad Sci USA 106(10):3776-3781.
  10. Morcos F, et al. (2010) Modeling conformational ensembles of slow functional motions in Pin1-WW. PLoS Computational Biology 6(12):e1001015.
  11. Bowman GR & Geissler PL (2012) Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites. Proc Natl Acad Sci USA 109(29):11681-11686.
  12. Silva DA, Bowman GR, Sosa-Peinado A, & Huang X (2011) A role for both conformational selection and induced fit in ligand binding by the LAO protein. PLoS Computational Biology 7(5):e1002054.
  13. Buch I, Giorgino T, & De Fabritiis G (2011) Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci USA 108(25):10184-10189.
  14. Held M, Metzner P, Prinz JH, & Noe F (2011) Mechanisms of protein-ligand association and its modulation by protein mutations. Biophysics Journal 100(3):701-710.
  15. Levin AM et al. (2012) Exploiting a natural conformational switch to engineer an interleukin-2 ‘super-kine.’ Nature 484(7395):529-533.