Molecular dynamics landscapes

JM Troyer, EE Cohen. Protein conformational landscapes Energy minimization and clustering of a long molecular dynamics trajectory. Proteins 23 97-110, 1995. 

Higo, J., Galzitskaya, O. V., Ono, S., and Nakamura, H. (2001). Energy landscape of a /3-hairpin peptide in explicit water studied by multicanonical molecular dynamics. Chem. Phys. Lett. 337, 169-175. 

Daidone, I., Amadei, A., Roccatano, D., Nola, A. D., Molecular dynamics simulation of protein folding by essential dynamics sampling folding landscape of horse heart cytochrome c, Biophys. J. 2003, 85, 2865-2871... 

Tsai, H. H., Reches, M., Tsai, C.J., Gunasekaran, K., Gazit, E., and Nussinov, R. (2005). Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation Significant role of Asn ladder. Proc. Natl. Acad. Sci. USA 102, 8174-8179. 

Nguyen, P.H., Mu, Y., and Stock, G. (2005) Structure and energy landscape of a photoswitchable peptide A replica exchange molecular dynamics study. Proteins 60, 485 194. 

Development of time-dependent DFS studies have to await further technological challenges in AFM where the lag phase of a mechanical contraption like a tip of AFM probe riding on a cantilever hovering over the rugged surface of a protein anchored on a platform by its very nature is slow compared to time-scales involved in the conformational dynamics from one peak to another in the energy landscape of a protein. As we encountered similar problems in molecular dynamics (MD), density functional studies (DFT), and 3D multi-nuclear NMR studies, analysis of voluminous data is very tedious. 

He J, Zhang Z, Shi Y, Liu H (2003) Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions. J. Chem. Phys. 119(7) 4005-4017... 

To address the docking problem, techniques for a more global exploration of the en-ag/ landscape are required. A variety of methods is available, frequently used in the context cf other modeling applications and optimization problems as well. Three major classes may be distinguished Monte Carlo techniques, molecular dynamics simulations, and genetic algorithms. Many different vari-fants exist for all of them and frequently, in... 

JE has shown considerable promise in steered molecular dynamics studies of the free energy landscape, and in particular it has become a popular choice for protein unfolding dynamics probably partly due to the exciting experiments carried out soon after its discovery. In this regard, the unfolding of deca-alanine has provided a relatively simple, yet realistic model that has been used to compare and test different approaches. -i"°-i5 -i i... 

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