162 lines
4.6 KiB
BibTeX
162 lines
4.6 KiB
BibTeX
@STRING{CELL="Cell"}
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@STRING{JMB="J. Mol. Biol."}
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@STRING{BIOCHEMISTRY="Biochemistry"}
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@STRING{BIOPHYSICALCHEMISTRY="Biophys. Chem."}
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@STRING{JCP="J. Chem. Phys."}
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@STRING{PNAS="Proc. Natl. Acad. Sci. USA"}
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@STRING{BIOPOLYMERS="Biopolymers"}
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@STRING{SCIENCE="Science"}
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@STRING{MMBR="Microbiol. Mol. Biol. R."}
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@STRING{NATURE="Nature"}
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@STRING{NATSTRUCTBIOL="Nat. Struct. Biol."}
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@STRING{NATBIOTECHNOL="Nat. Biotechnol."}
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@STRING{JBIOLCHEM="J. Biol. Chem."}
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@STRING{JSTRUCTBIOL="J. Struct. Biol."}
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@STRING{FOLDINGANDDESIGN="Folding and Design"}
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%@STRING{PROTSTRFUNCGEN="Prot. Str. Func. Gen."}
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@STRING{PROTSTRFUNCGEN="Proteins"}
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@STRING{PRL="Phys. Rev. Lett."}
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@STRING{TIBS="Trends in Biochem. Sci."}
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@STRING{EMBOJ="EMBO J."}
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@STRING{FEBS="FEBS Letters"}
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@STRING{FASEB="FASEB"}
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@STRING{JBIOCHEMTOXICOL="J. Biochem. Toxicol."}
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@STRING{CRBMB="Crit. Rev. Biochem. Mol. Biol."}
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@STRING{CHEMREV="Chem. Rev."}
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@STRING{ANNUREVBIOCHEM="Annu. Rev. Biochem."}
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% ------------------ books ----------------------
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@INBOOK{vanKampenBook,
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AUTHOR="van Kampen, N. G.",
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TITLE="Stochastic Processes in Physics and Chemistry, 2nd Edition",
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PUBLISHER="North Holland",
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PAGES={96--127},
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MONTH="July",
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DAY="1",
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YEAR=2001
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}
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@ARTICLE{LAMMPS,
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AUTHOR="S. Plimpton",
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TITLE="Fast Parallel Algorithms for Short-Range Molecular Dynamics",
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JOURNAL="J. Comp. Phys.",
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VOLUME=117,
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PAGES={1--19},
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YEAR="1995",
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NOTE={\url{http://lammps.sandia.gov/}}
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}
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@ARTICLE{packmol,
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AUTHOR="Martínez, L. and Andrade, R. and Brigin, E. G. and Martínez, J. M.",
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TITLE="Packmol: A package for building initial configurations for molecular dynamics simulations.",
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JOURNAL="J. Comp. Chem.",
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VOLUME=30,
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NUMBER=13,
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PAGES={2157--2164},
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YEAR=2009,
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NOTE={\url{http://www.ime.unicamp.br/~martinez/packmol/}}
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}
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%% The primary VMD citation, should be used by all publications using VMD
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@article{VMD,
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author={William Humphrey and Andrew Dalke and Klaus Schulten},
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title={{VMD} -- {V}isual {M}olecular {D}ynamics},
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journal={Journal of Molecular Graphics},
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year=1996,
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volume=14,
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pages={33-38},
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tbstatus={Published.},
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techrep={},
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tbreference={222},
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NOTE={\url{http://www.ks.uiuc.edu/Research/vmd}}
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}
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%% Interactive Molecular Dynamics, cited by papers doing IMD simulations
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@inproceedings{VMDIMD,
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author={John Stone and Justin Gullingsrud and Paul Grayson and Klaus Schulten},
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title={A System for Interactive Molecular Dynamics Simulation},
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booktitle={2001 ACM Symposium on Interactive 3D Graphics},
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publisher={ACM SIGGRAPH},
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address={New York},
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editor={John F. Hughes and Carlo H. S\'equin},
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pages={191-194},
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year={2001},
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note={},
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tbreference={304},
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tbstatus={Published.},
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annote={This symposium took place between March 19-21, 2001. {ISBN} 1-58113-292-1.}
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}
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@MISC{topotools,
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AUTHOR="Axel Kohlmeyer",
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TITLE="{The TopoTools VMD plugin}",
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HOWPUBLISHED={\url{http://sites.google.com/site/akohlmey/software/topotools/}}
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}
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@MISC{pizzapy,
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AUTHOR="Steve Plimpton",
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TITLE="{The Pizza.py toolkit}",
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HOWPUBLISHED={\url{http://www.cs.sandia.gov/~sjplimp/pizza.html}}
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}
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@ARTICLE{TraPPE,
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AUTHOR="Marcus G. Martin and J. Ilja Siepmann",
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TITLE="Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes",
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JOURNAL="J. Phys. Chem. B",
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VOLUME=102,
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NUMBER=14,
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PAGES={2569--2577},
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YEAR=1998
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}
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@ARTICLE{Raviv++SafinyaBiophysJ2007,
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AUTHOR="Uri Raviv and Toan Nguyen and Rouzbeh Ghafouri and Daniel J. Needleman and Youli Li and Herbert P. Miller and Leslie Wilson and Robijn F. Bruinsma and Cyrus R. Safinya",
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TITLE="Microtubule Protofilament Number Is Modulated in a Stepwise Fashion by the Charge Density of an Enveloping Layer",
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JOURNAL="Biophys. J.",
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VOLUME=92,
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NUMBER=1,
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PAGES={278--287},
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YEAR="2007",
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MONTH={January},
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DAY={1}
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}
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@ARTICLE{Raviv++SafinyaPNAS2005,
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AUTHOR="Uri Raviv and Daniel J. Needleman and Youli Li and Herbert P. Miller and Leslie Wilson and Cyrus R. Safinya",
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TITLE="Cationic liposome-microtubule complexes: Pathways to the formation of two-state lipid-protein nanotubes with open or closed ends",
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JOURNAL="Proc. Natl. Acad. Sci. USA",
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VOLUME=102,
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NUMBER=32,
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PAGES={11167--11172},
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YEAR="2005",
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MONTH={August},
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DAY={9}
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}
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@ARTICLE{Berendsen++StraatsmaJPhysChem1987,
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AUTHOR="H. J. C. Berendsen and J. R. Grigera and T. P. Straatsma",
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TITLE="The Missing Term in Effective Pair Potentials",
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JOURNAL="J. Phys. Chem.",
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VOLUME=91,
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NUMBER=24,
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PAGES={6269--6271},
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YEAR="1987",
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}
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@ARTICLE{Klimov+ThirumalaiPRL1997,
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AUTHOR="Klimov, D. K. and Thirumalai, D.",
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JOURNAL="Phys. Rev. Lett.",
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VOLUME=79,
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PAGES={317--320},
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YEAR="1997"
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}
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