Comments (4)
Note to users: Let us know if you use this software in your manuscript! We'd love to add it to this list.
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@article{Gao2017,
doi = {10.1021/acs.jpcb.7b00062},
url = {https://doi.org/10.1021%2Facs.jpcb.7b00062},
year = {2017},
month = {mar},
publisher = {American Chemical Society ({ACS})},
author = {Kaifu Gao and Yunjie Zhao},
title = {A Network of Conformational Transitions in the Apo Form of {NDM}-1 Enzyme Revealed by {MD} Simulation and a Markov State Model},
journal = {The Journal of Physical Chemistry B}
}
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@article{MSultan2017,
doi = {10.1021/acs.jctc.7b00182},
url = {https://doi.org/10.1021%2Facs.jctc.7b00182},
year = {2017},
month = {apr},
publisher = {American Chemical Society ({ACS})},
author = {Mohammad M. Sultan and Vijay S. Pande},
title = {{tICA}-Metadynamics: Accelerating Metadynamics by using kinetically selected collective variables},
journal = {Journal of Chemical Theory and Computation}
}
cc @msultan
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@article{MSultan2017,
doi = {10.1101/158592},
url = {https://doi.org/10.1101/158592},
year = {2017},
month = {jul},
publisher = {Cold Spring Harbor Laboratory},
author = {Mohammad Muneeb Sultan and Vijay Pande},
title = {Transferable {tICA}-Metadynamics: Efficient sampling of protein mutants by transferring information from the wild type{\textquotesingle}s Markov state model}
}
cc @msultan
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Related Issues (20)
- Implement Joy Plots HOT 9
- seaborn.apionly is deprecated HOT 2
- Adding 2D tIC trajectory visualization HOT 3
- Argument for time units in visualizations HOT 4
- plot_msm_network and plot_tpaths problems when msm is not 100% ergodic HOT 2
- Use of undirected graph in plot_msm_network HOT 4
- AttributeError: module 'msmexplorer' has no attribute 'plot_implied_timescales' HOT 3
- Fix coveralls
- plot_free_energy_2d.py fails with "ValueError: a and p must have same size" HOT 8
- MSMExplorer Installation: conflict error 'numba' HOT 1
- pip install error: No module named 'basesetup' HOT 1
- Add free energy plots using GMM models
- What are the numbers plotted on the axis of the histogram plot HOT 1
- No module named 'corner' HOT 1
- Plotting transition pathway using MSM and projected on tICs
- ImportError: cannot import name '_scipy_univariate_kde' from 'seaborn.distributions' HOT 1
- Installation of msmexplorer
- type object 'Dataset' has no attribute 'unify_chunks' HOT 2
- Add implied timescales plot to notebook HOT 4
- Port some of the schrodinger's plots HOT 7
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