msm.bib

@article{2010-everything-msm-afraid-ask,
    title = {Everything you wanted to know about Markov State Models but
        were afraid to ask},
	volume = {52},
	issn = {1046-2023},
	doi = {10.1016/j.ymeth.2010.06.002},
	number = {1},
	journal = {Methods},
	author = {Pande, Vijay S. and Beauchamp, Kyle and Bowman, Gregory R.},
	year = {2010},
	pages = {99 -- 105}
}


@article{2013-milliseconds-folding,
    title = {To milliseconds and beyond: challenges in the simulation of
        protein folding},
	volume = {23},
	issn = {1879-033X},
	shorttitle = {To milliseconds and beyond},
	doi = {10.1016/j.sbi.2012.11.002},
	language = {eng},
	number = {1},
	journal = {Curr. Opin. Struct. Biol.},
    author = {Lane, Thomas J. and Shukla, Diwakar and Beauchamp, Kyle A.
        and Pande, Vijay S.},
	month = feb,
	year = {2013},
	pmid = {23237705},
	pmcid = {PMC3673555},
	pages = {58--65}
}

@article{2014-msm-perspective,
    title = {Perspective: Markov models for long-timescale biomolecular
        dynamics},
	volume = {141},
	issn = {0021-9606, 1089-7690},
	shorttitle = {Perspective},
	doi = {10.1063/1.4895044},
	number = {9},
	journal = {J. Chem. Phys.},
	author = {Schwantes, C. R. and McGibbon, R. T. and Pande, V. S.},
	month = sep,
	year = {2014},
	pages = {090901}
}

@article{2015-gmrq,
	doi = {10.1063/1.4916292},
	year = 2015,
	month = {mar},
	publisher = {{AIP} Publishing},
	volume = {142},
	number = {12},
	pages = {124105},
	author = {Robert T. McGibbon and Vijay S. Pande},
	title = {Variational cross-validation of slow dynamical modes in molecular kinetics},
	journal = {J. Chem. Phys.}
}

@article{2014-noe-variational,
	doi = {10.1021/ct4009156},
	year = 2014,
	month = {apr},
	publisher = {American Chemical Society ({ACS})},
	volume = {10},
	number = {4},
	pages = {1739--1752},
    author = {Feliks N\"{u}ske and Bettina G. Keller and Guillermo
        P{\'{e}}rez-Hern{\'{a}}ndez and Antonia S. J. S. Mey and Frank
            No{\'{e}}},
	title = {Variational Approach to Molecular Kinetics},
	journal = {J. Chem. Theory Comput.}
}

@article{2014-chodera-msm,
	title = {Markov state models of biomolecular conformational dynamics},
	volume = {25},
	issn = {0959-440X},
	doi = {10.1016/j.sbi.2014.04.002},
	journal = {Curr. Opin. Struct. Biol.},
	author = {Chodera, John D and No{\'e}, Frank},
	month = apr,
	year = {2014},
	pages = {135--144}
}

@article{2011-prinz,
	title = {Markov models of molecular kinetics: Generation and validation},
	volume = {134},
	issn = {0021-9606, 1089-7690},
	url = {http://scitation.aip.org/content/aip/journal/jcp/134/17/10.1063/1.3565032},
	doi = {10.1063/1.3565032},
	number = {17},
	journal = {J. Chem. Phys.},
    author = {Prinz, Jan-Hendrik and Wu, Hao and Sarich, Marco and Keller,
        Bettina and Senne, Martin and Held, Martin and Chodera, John D. and
            Sch{\"u}tte, Christof and No{\'e}, Frank},
	month = may,
	year = {2011},
	pages = {174105}
}

@article{2014-kohlhoff-exacycle,
    title = {Cloud-based simulations on Google Exacycle reveal ligand
        modulation of {GPCR} activation pathways},
	volume = {6},
	copyright = {{\textcopyright} 2013 Nature Publishing Group},
	issn = {1755-4330},
	url = {http://www.nature.com/nchem/journal/v6/n1/full/nchem.1821.html},
	doi = {10.1038/nchem.1821},
	language = {en},
	number = {1},
	journal = {Nature Chem.},
    author = {Kohlhoff, Kai J. and Shukla, Diwakar and Lawrenz, Morgan and
        Bowman, Gregory R. and Konerding, David E. and Belov, Dan and
            Altman, Russ B. and Pande, Vijay S.},
	month = jan,
	year = {2014},
	pages = {15--21}
}

@article{2000-fah,
	title = {Screen Savers of the World Unite!},
	volume = {290},
	issn = {0036-8075, 1095-9203},
	url = {http://www.sciencemag.org/content/290/5498/1903},
	doi = {10.1126/science.290.5498.1903},
	language = {en},
	number = {5498},
	journal = {Science},
	author = {Shirts, Michael and Pande, Vijay S.},
	month = dec,
	year = {2000},
	pmid = {17742054},
	pages = {1903--1904}
}

@article{2008-anton,
	title = {Anton, a Special-purpose Machine for Molecular Dynamics Simulation},
	volume = {51},
	issn = {0001-0782},
	url = {http://doi.acm.org/10.1145/1364782.1364802},
	doi = {10.1145/1364782.1364802},
	number = {7},
	journal = {Commun. ACM},
    author = {Shaw, David E. and Deneroff, Martin M. and Dror, Ron O. and
        Kuskin, Jeffrey S. and Larson, Richard H. and Salmon, John K. and
            Young, Cliff and Batson, Brannon and Bowers, Kevin J. and Chao,
        Jack C. and Eastwood, Michael P. and Gagliardo, Joseph and
            Grossman, J. P. and Ho, C. Richard and Ierardi, Douglas J. and
            Kolossv{\'a}ry, Istv{\'a}n and Klepeis, John L. and Layman,
        Timothy and McLeavey, Christine and Moraes, Mark A. and Mueller,
        Rolf and Priest, Edward C. and Shan, Yibing and Spengler, Jochen
            and Theobald, Michael and Towles, Brian and Wang, Stanley C.},
	month = jul,
	year = {2008},
	pages = {91--97}
}

@article{2010-gpugrid,
    title = {High-Throughput All-Atom Molecular Dynamics Simulations Using
        Distributed Computing},
	volume = {50},
	issn = {1549-9596},
	doi = {10.1021/ci900455r},
	number = {3},
	journal = {J. Chem. Inf. Model.},
    author = {Buch, I. and Harvey, M. J. and Giorgino, T. and Anderson, D.
        P. and De Fabritiis, G.},
	month = mar,
	year = {2010},
	pages = {397--403}
}

@article{2009-friedrichs-gpu,
	title = {Accelerating molecular dynamic simulation on graphics processing units},
	volume = {30},
	copyright = {Copyright {\textcopyright} 2009 Wiley Periodicals, Inc.},
	issn = {1096-987X},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/jcc.21209/abstract},
	doi = {10.1002/jcc.21209},
	language = {en},
	number = {6},
	journal = {J. Comput. Chem.},
    author = {Friedrichs, Mark S. and Eastman, Peter and Vaidyanathan,
        Vishal and Houston, Mike and Legrand, Scott and Beberg, Adam L. and
            Ensign, Daniel L. and Bruns, Christopher M. and Pande, Vijay
            S.},
	month = apr,
	year = {2009},
	pages = {864--872}
}

@book{2014-msm-book,
    title = {An Introduction to Markov State Models and Their Application
        to Long Timescale Molecular Simulation},
	volume = {797},
	url = {http://publications.mi.fu-berlin.de/1360/},
	publisher = {Springer},
	author = {Bowman, G. R. and Pande, V. S. and No{\'e}, F.},
	editor = {Bowman, G. R. and Pande, V. S. and No{\'e}, F.},
	year = {2014}
}

@article{2015-ratematrix,
    Author = {McGibbon, Robert T. and Pande, Vijay S.},
    Doi = {10.1063/1.4926516},
    Eid = 034109,
    Journal = {J. Chem. Phys.},
    Number = {3},
    Pages = {034109},
    Title = {Efficient maximum likelihood parameterization of continuous-time
        Markov processes},
    Url = {http://scitation.aip.org/content/aip/journal/jcp/143/3/10.1063/1.4926516},
    Volume = {143},
    Year = {2015}
}

@article{2005-pcca,
    author = {Deuflhard, Peter and Weber, Marcus},
    doi = {10.1016/j.laa.2004.10.026},
    issn = {00243795},
    journal = {Linear Algebra Appl.},
    month = {mar},
    pages = {161--184},
    title = {{Robust Perron cluster analysis in conformation dynamics}},
    url = {http://www.sciencedirect.com/science/article/pii/S0024379504004689},
    volume = {398},
    year = {2005}
}

@article{2013-schwantes-tica,
    Author = {Christian R. Schwantes and Vijay S. Pande},
    Doi = {10.1021/ct300878a},
    Journal = {J. Chem. Theory Comput.},
    Number = {4},
    Pages = {2000-2009},
    Title = {Improvements in Markov State Model Construction Reveal Many
        Non-Native Interactions in the Folding of NTL9},
    Url = {http://dx.doi.org/10.1021/ct300878a},
    Volume = {9},
    Year = {2013}
}

@article{2013-noe-tica,
    Author = {P{\'e}rez-Hern{\'a}ndez, Guillermo and Paul, Fabian and Giorgino,
        Toni and De Fabritiis, Gianni and No{\'e}, Frank},
    Doi = {10.1063/1.4811489},
    Journal = {J. Chem. Phys.},
    Number = {1},
    Pages = {015102},
    Title = {Identification of slow molecular order parameters for Markov model
        construction},
    Url = {http://scitation.aip.org/content/aip/journal/jcp/139/1/10.1063/1.4811489},
    Volume = {139},
    Year = {2013}
}

@Unpublished{2016-sparsetica,
    Author = {McGibbon, Robert T. and Pande, Vijay S.},
    Title = {Identification of simple reaction coordinates from complex dynamics},
    Year = {2016},
    Month = {March},
    eprint = {1602.08776},
    archivePrefix = {arXiv},
}

% todo: doi
@inproceedings{2014-hmm,
    Author = {McGibbon, Robert T. and Ramsundar, Bharath and Sultan, Mohammad
        M. and Kiss, Gert and Pande, Vijay S.},
    Booktitle = {Proceedings of The 31st International Conference on Machine
        Learning},
    Pages = {1197-1205},
    Title = {Understanding Protein Dynamics with L1-Regularized Reversible
        Hidden Markov Models},
    Year = {2014},
}

@article{2012-drid,
    Author = {Ting Zhou and Amedeo Caflisch},
    Doi = {10.1021/ct3003145},
    Journal = {J. Chem. Theory Comput.},
    Number = {8},
    Pages = {2930-2937},
    Title = {Distribution of Reciprocal of Interatomic Distances: A Fast
        Structural Metric},
    Volume = {8},
    Year = {2012},
}