Peter Minary : Publications

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@article{knapp2015exploring,
  title = "Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo",
  author = "Knapp, Bernhard and Demharter, Samuel and Deane, Charlotte M and Minary, Peter",
  year = "2015",
  journal = "Bioinformatics",
  pages = "btv502",
  publisher = "Oxford University Press",
}

@article{minary2014training,
  title = "Training-free atomistic prediction of nucleosome occupancy",
  author = "Minary, Peter and Levitt, Michael",
  year = "2014",
  journal = "Proceedings of the National Academy of Sciences",
  number = "17",
  pages = "6293--6298",
  publisher = "National Acad Sciences",
  volume = "111",
}

@article{sim2012modeling,
  title = "Modeling and design by hierarchical natural moves",
  author = "Sim, Adelene YL and Levitt, Michael and Minary, Peter",
  year = "2012",
  journal = "Proceedings of the National Academy of Sciences",
  number = "8",
  pages = "2890--2895",
  publisher = "National Acad Sciences",
  volume = "109",
}

@article{zhang2012multiscale,
  title = "Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images",
  author = "Zhang, Junjie and Minary, Peter and Levitt, Michael",
  year = "2012",
  journal = "Proceedings of the National Academy of Sciences",
  number = "25",
  pages = "9845--9850",
  publisher = "National Acad Sciences",
  volume = "109",
}

@article{sim2012modeling,
  title = "Modeling nucleic acids",
  author = "Sim, Adelene YL and Minary, Peter and Levitt, Michael",
  year = "2012",
  journal = "Current Opinion in Structural Biology",
  publisher = "Elsevier",
}

@article{minary2010conformational,
  title = "Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm",
  author = "Minary, Peter and Levitt, Michael",
  year = "2010",
  journal = "Journal of Computational Biology",
  number = "8",
  pages = "993--1010",
  publisher = "Mary Ann Liebert, Inc. 140 Huguenot Street, 3rd Floor New Rochelle, NY 10801 USA",
  volume = "17",
}

@article{minary2008probing,
  title = "Probing protein fold space with a simplified model",
  author = "Minary, Peter and Levitt, Michael",
  year = "2008",
  journal = "Journal of molecular biology",
  number = "4",
  pages = "920",
  publisher = "NIH Public Access",
  volume = "375",
}

@article{minary2008dynamical,
  title = "Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure",
  author = "Minary, Peter and Tuckerman, Mark E and Martyna, Glenn J",
  year = "2008",
  journal = "SIAM Journal on Scientific Computing",
  number = "4",
  pages = "2055--2083",
  publisher = "SIAM",
  volume = "30",
}

@article{minary2006discussion,
  title = "Discussion of" EQUI-energy sampler" by Kou, Zhou and Wong",
  author = "Minary, P and Levitt, M",
  year = "2006",
  journal = "Ann. Stat.",
  number = "math. ST/0611221",
  pages = "1636--1641",
  publisher = "math. ST/0507080",
  volume = "34",
}

@article{minary2005reaction,
  title = "Reaction Mechanism of cis-1, 3-Butadiene Addition to the Si (100)-2$\times$ 1 Surface",
  author = "Minary, Peter and Tuckerman, Mark E",
  year = "2005",
  journal = "Journal of the American Chemical Society",
  number = "4",
  pages = "1110--1111",
  publisher = "ACS Publications",
  volume = "127",
}

@article{iftimie2005ab,
  title = "Ab initio molecular dynamics: Concepts, recent developments, and future trends",
  author = "Iftimie, Radu and Minary, Peter and Tuckerman, Mark E",
  year = "2005",
  journal = "Proceedings of the National Academy of Sciences of the United States of America",
  number = "19",
  pages = "6654--6659",
  publisher = "National Acad Sciences",
  volume = "102",
}

@article{minary2004long,
  title = "Long range interactions on wires: A reciprocal space based formalism",
  author = "Min{\'a}ry, Peter and Morrone, Joseph A and Yarne, Dawn A and Tuckerman, Mark E and Martyna, Glenn J",
  year = "2004",
  journal = "The Journal of chemical physics",
  pages = "11949",
  volume = "121",
}

@article{minary2004reaction,
  title = "Reaction Pathway of the [4+ 2] Diels-Alder Adduct Formation on Si (100)-2$\times$ 1",
  author = "Minary, Peter and Tuckerman, Mark E",
  year = "2004",
  journal = "Journal of the American Chemical Society",
  number = "43",
  pages = "13920--13921",
  publisher = "ACS Publications",
  volume = "126",
}

@article{minary2004long,
  title = "Long time molecular dynamics for enhanced conformational sampling in biomolecular systems",
  author = "Minary, P and Tuckerman, ME and Martyna, GJ",
  year = "2004",
  journal = "Physical review letters",
  number = "15",
  pages = "150201",
  publisher = "APS",
  volume = "93",
}

@article{minary2003algorithms,
  title = "Algorithms and novel applications based on the isokinetic ensemble. II. Ab initio molecular dynamics",
  author = "Minary, Peter and Martyna, Glenn J and Tuckerman, Mark E",
  year = "2003",
  journal = "The Journal of chemical physics",
  pages = "2527",
  volume = "118",
}

@article{minary2003algorithms,
  title = "Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics",
  author = "Minary, Peter and Martyna, Glenn J and Tuckerman, Mark E",
  year = "2003",
  journal = "The Journal of chemical physics",
  pages = "2510",
  volume = "118",
}

@article{tuckerman2002new,
  title = "A new reciprocal space based treatment of long range forces on surfaces",
  author = "Tuckerman, ME and Minary, P and Pihakari, K and Martyna, GJ",
  year = "2002",
  journal = "J. Chem. Phys",
  pages = "5351",
  volume = "116",
}