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tools.bib
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@article{2014-lipid14,
doi = {10.1021/ct4010307},
year = 2014,
month = {feb},
publisher = {American Chemical Society ({ACS})},
volume = {10},
number = {2},
pages = {865--879},
author = {Callum J. Dickson and Benjamin D. Madej and {\AA}ge A. Skjevik
and Robin M. Betz and Knut Teigen and Ian R. Gould and Ross C. Walker},
title = {Lipid14: The Amber Lipid Force Field},
journal = {J. Chem. Theory Comput.}
}
@Article{2007-ipython,
Author = {P\'erez, Fernando and Granger, Brian E.},
Title = {{IP}ython: a System for Interactive Scientific Computing},
Journal = {IEE Comput. Sci. Eng},
Volume = {9},
Number = {3},
Pages = {21--29},
month = may,
year = 2007,
url = "http://ipython.org",
ISSN = "1521-9615",
doi = {10.1109/MCSE.2007.53},
publisher = {IEEE Computer Society},
}
@article{2016-charmm-gui,
doi = {10.1021/acs.jctc.5b00935},
url = {http://dx.doi.org/10.1021/acs.jctc.5b00935},
year = 2016,
month = {jan},
publisher = {American Chemical Society ({ACS})},
volume = {12},
number = {1},
pages = {405--413},
author = {Jumin Lee and Xi Cheng and Jason M. Swails and Min Sun Yeom and
Peter K. Eastman and Justin A. Lemkul and Shuai Wei and Joshua Buckner
and Jong Cheol Jeong and Yifei Qi and Sunhwan Jo and Vijay S. Pande
and David A. Case and Charles L. Brooks and Alexander D. MacKerell
and Jeffery B. Klauda and Wonpil Im},
title = {{CHARMM}-{GUI} Input Generator for {NAMD}, {GROMACS}, {AMBER},
{OpenMM}, and {CHARMM}/{OpenMM} Simulations Using the {CHARMM}36
Additive Force Field},
journal = {J. Chem. Theory Comput.}
}
@article{2015-gromacs,
doi = {10.1016/j.softx.2015.06.001},
year = 2015,
month = {sep},
publisher = {Elsevier {BV}},
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pages = {19--25},
author = {Mark James Abraham and Teemu Murtola and Roland Schulz and
Szil{\'{a}}rd P{\'{a}}ll and Jeremy C. Smith and Berk Hess and Erik
Lindahl},
title = {GROMACS: High performance molecular simulations through
multi-level parallelism from laptops to supercomputers},
journal = {SoftwareX}
}
@article{1992-wham,
doi = {10.1002/jcc.540130812},
year = 1992,
month = {oct},
publisher = {Wiley-Blackwell},
volume = {13},
number = {8},
pages = {1011--1021},
author = {Shankar Kumar and John M. Rosenberg and Djamal Bouzida and Robert
H. Swendsen and Peter A. Kollman},
title = {The weighted histogram analysis method for free-energy
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journal = {J. Comput. Chem.}
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@article{2015-mdtraj,
doi = {10.1016/j.bpj.2015.08.015},
year = 2015,
month = {oct},
publisher = {Elsevier {BV}},
volume = {109},
number = {8},
pages = {1528--1532},
author = {Robert~T. McGibbon and Kyle~A. Beauchamp and Matthew~P. Harrigan
and Christoph Klein and Jason~M. Swails and Carlos~X. Hern{\'{a}}ndez
and Christian~R. Schwantes and Lee-Ping Wang and Thomas~J. Lane and
Vijay~S. Pande},
title = {{MDTraj}: A Modern Open Library for the Analysis of Molecular
Dynamics Trajectories},
journal = {Biophys. J.}
}
@Article{2007-matplotlib,
Author = {Hunter, J. D.},
Title = {Matplotlib: A 2D graphics environment},
Journal = {Computing In Science \& Engineering},
Volume = {9},
Number = {3},
Pages = {90--95},
abstract = {Matplotlib is a 2D graphics package used for Python
for application development, interactive scripting, and
publication-quality image generation across user
interfaces and operating systems.},
doi = {10.5281/zenodo.44579},
publisher = {IEEE COMPUTER SOC},
year = 2007
}
@article {1995-stride,
author = {Frishman, Dmitrij and Argos, Patrick},
title = {Knowledge-based protein secondary structure assignment},
journal = {Proteins},
volume = {23},
number = {4},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
issn = {1097-0134},
doi = {10.1002/prot.340230412},
pages = {566--579},
year = {1995},
}
@article{1996-vmd,
author={William Humphrey and Andrew Dalke and Klaus Schulten},
title={{VMD} -- {V}isual {M}olecular {D}ynamics},
journal={J. Mol. Graphics},
volume=14,
pages={33-38},
doi = {10.1016/0263-7855(96)00018-5},
note={},
tbstatus={Published.},
techrep={},
tbreference={222}
}
@article{2013-openmm,
author = {Peter Eastman and Mark S. Friedrichs and John D. Chodera and Randall
J. Radmer and Christopher M. Bruns and Joy P. Ku and Kyle A. Beauchamp and
Thomas J. Lane and Lee-Ping Wang and Diwakar Shukla and Tony Tye and
Mike Houston and Timo Stich and Christoph Klein and Michael R. Shirts
and Vijay S. Pande},
title = {OpenMM 4: A Reusable, Extensible, Hardware Independent Library for
High Performance Molecular Simulation},
journal = {J. Chem. Theory Comput.},
volume = {9},
number = {1},
pages = {461-469},
year = {2013},
doi = {10.1021/ct300857j},
}
@article{2016-htmd,
author = {S. Doerr and M. J. Harvey and Frank Noé and G. De Fabritiis},
title = {HTMD: High-Throughput Molecular Dynamics for Molecular Discovery},
journal = {J. Chem. Theory Comput.},
volume = {12},
number = {4},
pages = {1845-1852},
year = {2016},
doi = {10.1021/acs.jctc.6b00049},
}
@article{2012-jemma,
doi = {10.1021/ct300274u},
url = {http://dx.doi.org/10.1021/ct300274u},
year = 2012,
month = {jul},
publisher = {American Chemical Society ({ACS})},
volume = {8},
number = {7},
pages = {2223--2238},
author = {Martin Senne and Benjamin Trendelkamp-Schroer and Antonia
S.J.S. Mey and Christof Schütte and Frank No{\'{e}}},
title = {{EMMA}: A Software Package for Markov Model Building and Analysis},
journal = {J. Chem. Theory Comput.}
}
@article{2015-pyemma,
doi = {10.1021/acs.jctc.5b00743},
year = 2015,
month = {nov},
publisher = {American Chemical Society ({ACS})},
volume = {11},
number = {11},
pages = {5525--5542},
author = {Martin K. Scherer and Benjamin Trendelkamp-Schroer and Fabian
Paul and Guillermo P{\'{e}}rez-Hern{\'{a}}ndez and Moritz Hoffmann and
Nuria Plattner and Christoph Wehmeyer and Jan-Hendrik Prinz and
Frank No{\'{e}}},
title = {{PyEMMA} 2: A Software Package for Estimation, Validation, and
Analysis of Markov Models},
journal = {J. Chem. Theory Comput.}
}
@inproceedings{2010-minibatch-kmeans,
doi = {10.1145/1772690.1772862},
url = {http://dx.doi.org/10.1145/1772690.1772862},
year = 2010,
publisher = {Association for Computing Machinery ({ACM})},
author = {D. Sculley},
title = {Web-scale k-means clustering},
booktitle = {Proceedings of the 19th international conference on world wide web}
}
@article{2009-msmbuilder1,
doi = {10.1016/j.ymeth.2009.04.013},
url = {http://dx.doi.org/10.1016/j.ymeth.2009.04.013},
year = 2009,
month = {oct},
publisher = {Elsevier {BV}},
volume = {49},
number = {2},
pages = {197--201},
author = {Gregory R. Bowman and Xuhui Huang and Vijay S. Pande},
title = {Using generalized ensemble simulations and Markov state models
to identify conformational states},
journal = {Methods}
}
@article{2011-msmbuilder2,
title = {{MSMBuilder}2: Modeling Conformational Dynamics on the
Picosecond to Millisecond Scale},
volume = {7},
issn = {1549-9618},
shorttitle = {{MSMBuilder}2},
doi = {10.1021/ct200463m},
number = {10},
journal = {J. Chem. Theory Comput.},
author = {Beauchamp, Kyle A. and Bowman, Gregory R. and Lane, Thomas J.
and Maibaum, Lutz and Haque, Imran S. and Pande, Vijay S.},
month = oct,
year = {2011},
pages = {3412--3419}
}
@article{2016-msmbuilder3.5-zenodo,
author = {Robert T. McGibbon and
Matthew Harrigan and
Bharath Ramsundar and
Kyle Beauchamp and
msultan and
Carlos Hernández and
Christian Schwantes and
peastman and
Brooke Husic and
pfrstg and
Steven Kearnes and
Joshua Adelman and
gkiss},
title = {MSMBuilder 3.5},
month = jun,
year = 2016,
doi = {10.5281/zenodo.55601},
url = {http://dx.doi.org/10.5281/zenodo.55601}
}
@misc{2016-osprey,
author = {Robert T. McGibbon and
Carlos X. Hernández and
Matthew P. Harrigan and
Steven Kearnes and
Mohammad M. Sultan and
Stanislaw Jastrzebski and
Brooke E. Husic and
Vijay S. Pande},
title = {Osprey 1.0.0},
month = jun,
year = 2016,
doi = {10.5281/zenodo.56251},
url = {http://dx.doi.org/10.5281/zenodo.56251}
}