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Peter Minary, Ph.D. - Publications

Affiliations: 
2005 New York University, New York, NY, United States 
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Chang JY, Cui Z, Yang K, Huang J, Minary P, Zhang J. Hierarchical Natural Move Monte Carlo Refines Flexible RNA Structures into Cryo-EM Densities. Rna (New York, N.Y.). PMID 32826323 DOI: 10.1261/Rna.071100.119  0.321
2016 Demharter S, Knapp B, Deane CM, Minary P. Modeling Functional Motions of Biological Systems by Customized Natural Moves. Biophysical Journal. 111: 710-21. PMID 27558715 DOI: 10.1016/J.Bpj.2016.06.028  0.328
2014 Minary P, Levitt M. Training-free atomistic prediction of nucleosome occupancy. Proceedings of the National Academy of Sciences of the United States of America. 111: 6293-8. PMID 24733939 DOI: 10.1073/Pnas.1404475111  0.415
2012 Zhang J, Minary P, Levitt M. Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images. Proceedings of the National Academy of Sciences of the United States of America. 109: 9845-50. PMID 22665770 DOI: 10.1073/Pnas.1205945109  0.47
2012 Sim AY, Minary P, Levitt M. Modeling nucleic acids. Current Opinion in Structural Biology. 22: 273-8. PMID 22538125 DOI: 10.1016/J.Sbi.2012.03.012  0.468
2012 Sim AY, Levitt M, Minary P. Modeling and design by hierarchical natural moves. Proceedings of the National Academy of Sciences of the United States of America. 109: 2890-5. PMID 22308445 DOI: 10.1073/Pnas.1119918109  0.472
2010 Minary P, Levitt M. Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 993-1010. PMID 20726792 DOI: 10.1089/Cmb.2010.0016  0.483
2008 Minary P, Levitt M. Probing protein fold space with a simplified model. Journal of Molecular Biology. 375: 920-33. PMID 18054792 DOI: 10.1016/J.Jmb.2007.10.087  0.425
2007 Minary P, Tuckerman ME, Martyna GJ. Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure Siam Journal On Scientific Computing. 30: 2055-2083. DOI: 10.1137/070686706  0.57
2006 Minary P, Levitt M. Discussion of "equi-energy sampler" by Kou, Zhou and Wong Annals of Statistics. 34: 1636-1641. DOI: 10.1214/009053606000000470  0.485
2005 Iftimie R, Minary P, Tuckerman ME. Ab initio molecular dynamics: Concepts, recent developments, and future trends Proceedings of the National Academy of Sciences of the United States of America. 102: 6654-6659. PMID 15870204 DOI: 10.1073/Pnas.0500193102  0.568
2005 Minary P, Tuckerman ME. Reaction mechanism of cis-1,3-butadiene addition to the Si(100)-2 x 1 surface. Journal of the American Chemical Society. 127: 1110-1. PMID 15669844 DOI: 10.1021/Ja046934V  0.55
2005 Minary P, Tuckerman ME. Reaction mechanism of cis-1,3-butadiene addition to the Si(100)-2 x 1 surface Journal of the American Chemical Society. 127: 1110-1111. DOI: 10.1021/ja046934v  0.452
2004 Mináry P, Morrone JA, Yarne DA, Tuckerman ME, Martyna GJ. Long range interactions on wires: a reciprocal space based formalism. The Journal of Chemical Physics. 121: 11949-56. PMID 15634157 DOI: 10.1063/1.1806403  0.545
2004 Minary P, Tuckerman ME, Martyna GJ. Long time molecular dynamics for enhanced conformational sampling in biomolecular systems Physical Review Letters. 93: 150201-1-150201-4. PMID 15524853 DOI: 10.1103/Physrevlett.93.150201  0.553
2004 Minary P, Tuckerman ME. Reaction pathway of the [4 + 2] Diels-Alder adduct formation on Si(100)-2 x 1. Journal of the American Chemical Society. 126: 13920-1. PMID 15506742 DOI: 10.1021/Ja046522M  0.564
2004 Mináry P, Morrone JA, Yame DA, Tuckerman ME, Martyna GJ. Long range interactions on wires: A reciprocal space based formalism Journal of Chemical Physics. 121: 11949-11956. DOI: 10.1063/1.1806403  0.442
2004 Minary P, Tuckerman ME. Reaction pathway of the [4 + 2] diels-alder adduct formation on Si(100)-2x1 Journal of the American Chemical Society. 126: 13920-13921. DOI: 10.1021/ja046522m  0.432
2003 Minary P, Martyna GJ, Tuckerman ME. Algorithms and novel applications based on the isokinetic ensemble. II. Ab initio molecular dynamics Journal of Chemical Physics. 118: 2527-2538. DOI: 10.1063/1.1534583  0.58
2003 Minary P, Martyna GJ, Tuckerman ME. Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics Journal of Chemical Physics. 118: 2510-2526. DOI: 10.1063/1.1534582  0.555
2002 Mináry P, Tuckerman ME, Pihakari KA, Martyna GJ. A new reciprocal space based treatment of long range interactions on surfaces Journal of Chemical Physics. 116: 5351-5362. DOI: 10.1063/1.1453397  0.538
2002 Rosso L, Mináry P, Zhu Z, Tuckerman ME. On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles Journal of Chemical Physics. 116: 4389-4402. DOI: 10.1063/1.1448491  0.677
2000 Mináry P, Jedlovszky P, Mezei M, Turi L. A Comprehensive Liquid Simulation Study of Neat Formic Acid The Journal of Physical Chemistry B. 104: 8287-8294. DOI: 10.1021/Jp000205U  0.333
2000 Turi L, Mináry P, Rossky PJ. Non-linear response and hydrogen bond dynamics for electron solvation in methanol Chemical Physics Letters. 316: 465-470. DOI: 10.1016/S0009-2614(99)01328-7  0.316
1999 Mináry P, Turi L, Rossky PJ. Nonadiabatic molecular dynamics simulation of photoexcitation experiments for the solvated electron in methanol Journal of Chemical Physics. 110: 10953-10962. DOI: 10.1063/1.479032  0.309
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