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Nature, ISSN 0028-0836, 12/2005, Volume 438, Issue 7069, pp. 803 - 819
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 04/2019, Volume 150, Issue 13, p. 134107
Markov state models (MSMs) provide some of the simplest mathematical and physical descriptions of dynamical and thermodynamical properties of complex systems.... 
MOLECULAR-DYNAMICS | LIGAND-BINDING | REDUCTION | HISTOGRAM ANALYSIS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | SYSTEMS | FREE-ENERGIES | TRANSITION-STATES | SIMULATION | Granulation | Computer simulation | Time series analysis | Molecular dynamics | Markov chains | Fluxes | Clustering | Complex systems | Relaxation time | Optimization
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 05/2019, Volume 123, Issue 17, pp. 3672 - 3678
Understanding ligand dissociation mechanisms at an atomic resolution is a highly desired but difficult to achieve objective in experiments as well as in... 
PATHWAYS | ACCURATE | MECHANISM | DYNAMICS | CHEMISTRY, PHYSICAL | OPTIMIZATION | RELIABILITY | PROTEINS | BINDING | STRUCTURE PREDICTION | ENTROPY
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 08/2018, Volume 149, Issue 7, p. 072324
Markov state models (MSMs) are more and more widely used in the analysis of molecular simulations to incorporate multiple trajectories together and obtain more... 
COARSE MASTER-EQUATIONS | HISTOGRAM ANALYSIS | KINETICS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | DYNAMICS | CHEMISTRY, PHYSICAL | FREE-ENERGIES
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 12/2017, Volume 13, Issue 12, p. 6328
We present an algorithm to calculate free energies and rates from molecular simulations on biased potential energy surfaces. As input, it uses the accumulated... 
Potential energy | Maximization | Preprocessing | Computer simulation | Molecular dynamics | Markov chains | Ribonucleic acid--RNA | Free energy | Molecular chains | Optimization | Bins | Simulation | Ion channels
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 12/2017, Volume 13, Issue 12, pp. 6328 - 6342
We present an algorithm to calculate free energies and rates from molecular simulations on biased potential energy surfaces. As input, it uses the accumulated... 
TRANSITION | ACCELERATED MOLECULAR-DYNAMICS | MONTE-CARLO DATA | KINETICS | EQUILIBRIUM | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | REPLICA EXCHANGE | FORCE-FIELDS | BAYESIAN-ANALYSIS | EFFICIENT
Journal Article
Physical Review X, ISSN 2160-3308, 2017, Volume 7, Issue 3, p. 031060
We present a method that enables the identification and analysis of conformational Markovian transition states from atomistic or coarse-grained molecular... 
PATHWAYS | MECHANICS | PEPTIDES | COMPLEX-SYSTEMS | MODELS | PHYSICS, MULTIDISCIPLINARY | DYNAMICS | DIFFUSION | FREE-ENERGIES | CHALLENGES | SURFACES
Journal Article
by Waterston, Robert H and Lindblad-Toh, Kerstin and Birney, Ewan and Rogers, Jane and Abril, Josep F and Agarwal, Pankaj and Agarwala, Richa and Ainscough, Rachel and Alexandersson, Marina and An, Peter and Antonarakis, Stylianos E and Attwood, John and Baertsch, Robert and Bailey, Jonathon and Barlow, Karen and Beck, Stephan and Berry, Eric and Birren, Bruce and Bloom, Toby and Bork, Peer and Botcherby, Marc and Bray, Nicolas and Brent, Michael R and Brown, Daniel G and Brown, Stephen D and Bult, Carol and Burton, John and Butler, Jonathan and Campbell, Robert D and Carninci, Piero and Cawley, Simon and Chiaromonte, Francesca and Chinwalla, Asif T and Church, Deanna M and Clamp, Michele and Clee, Christopher and Collins, Francis S and Cook, Lisa L and Copley, Richard R and Coulson, Alan and Couronne, Olivier and Cuff, James and Curwen, Val and Cutts, Tim and Daly, Mark and David, Robert and Davies, Joy and Delehaunty, Kimberly D and Deri, Justin and Dermitzakis, Emmanouil T and Dewey, Colin and Dickens, Nicholas J and Diekhans, Mark and Dodge, Sheila and Dubchak, Inna and Dunn, Diane M and Eddy, Sean R and Elnitski, Laura and Emes, Richard D and Eswara, Pallavi and Eyras, Eduardo and Felsenfeld, Adam and Fewell, Ginger A and Flicek, Paul and Foley, Karen and Frankel, Wayne N and Fulton, Lucinda A and Fulton, Robert S and Furey, Terrence S and Gage, Diane and Gibbs, Richard A and Glusman, Gustavo and Gnerre, Sante and Goldman, Nick and Goodstadt, Leo and Grafham, Darren and Graves, Tina A and Green, Eric D and Gregory, Simon and Guigó, Roderic and Guyer, Mark and Hardison, Ross C and Haussler, David and Hayashizaki, Yoshihide and LaHillier, Deana W and Hinrichs, Angela and Hlavina, Wratko and Holzer, Timothy and Hsu, Fan and Hua, Axin and Hubbard, Tim and Hunt, Adrienne and Jackson, Ian and Jaffe, David B and Johnson, L. Steven and Jones, Matthew and Jones, Thomas A and Joy, Ann and Kamal, Michael and Karlsson, Elinor K and ... and Mouse Genome Sequencing Consor and Mouse Genome Sequencing Consortium and Joint Genome Institute (JGI) and Naturvetenskapliga fakulteten and Department of Mathematical Statistics and Institutionen för matematisk statistik and Faculty of Sciences and Göteborgs universitet and Gothenburg University
Nature, ISSN 0028-0836, 12/2002, Volume 420, Issue 6915, pp. 520 - 562
Journal Article