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Nicolae-Viorel Buchete, Ph.D. - Publications

Affiliations: 
2003 Boston University, Boston, MA, United States 
Area:
protein dynamics and thermodynamics using theoretical and computational methods
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45 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 Narayan B, Yuan Y, Fathizadeh A, Elber R, Buchete NV. Long-time methods for molecular dynamics simulations: Markov State Models and Milestoning. Progress in Molecular Biology and Translational Science. 170: 215-237. PMID 32145946 DOI: 10.1016/Bs.Pmbts.2020.01.002  0.393
2019 Duffy F, Maheshwari N, Buchete NV, Shields D. Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein-Protein Interactions. Methods in Molecular Biology (Clifton, N.J.). 2001: 73-95. PMID 31134568 DOI: 10.1007/978-1-4939-9504-2_5  0.362
2018 Tywoniuk B, Yuan Y, McCartan S, Szydlowska BM, Tofoleanu F, Brooks BR, Buchete NV. Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer's Aβ Protofilaments. The Journal of Physical Chemistry. B. PMID 30335383 DOI: 10.1021/Acs.Jpcb.8B07423  0.748
2018 Narayan B, Herbert C, Yuan Y, Rodriguez BJ, Brooks BR, Buchete NV. Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides. The Journal of Chemical Physics. 149: 072323. PMID 30134732 DOI: 10.1063/1.5027580  0.412
2018 Tofoleanu F, Yuan Y, Pickard FC, Tywoniuk B, Brooks BR, Buchete NV. Structural Modulation of Human Amylin Protofilaments by Naturally-Occurring Mutations. The Journal of Physical Chemistry. B. PMID 29406755 DOI: 10.1021/Acs.Jpcb.7B12083  0.756
2017 Leahy CT, Kells A, Hummer G, Buchete NV, Rosta E. Peptide dimerization-dissociation rates from replica exchange molecular dynamics. The Journal of Chemical Physics. 147: 152725. PMID 29055328 DOI: 10.1063/1.5004774  0.386
2017 Martini L, Kells A, Covino R, Hummer G, Buchete N, Rosta E. Variational Identification of Markovian Transition States Physical Review X. 7. DOI: 10.1103/Physrevx.7.031060  0.391
2016 Sánchez-Sanz G, Tywoniuk B, Matallanas D, Romano D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV. SARAH Domain-Mediated MST2-RASSF Dimeric Interactions. Plos Computational Biology. 12: e1005051. PMID 27716844 DOI: 10.1371/Journal.Pcbi.1005051  0.716
2016 Leahy CT, Murphy RD, Hummer G, Rosta E, Buchete NV. Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers. The Journal of Physical Chemistry Letters. PMID 27323250 DOI: 10.1021/Acs.Jpclett.6B00518  0.427
2016 Crowe A, Sánchez-Sanz G, Tywoniuk B, Shields DC, Buchete N. Coarse Master Equation-Based Analysis of N-Methylation and Temperature Effects on the Dynamics of Cyclic Peptides Biophysical Journal. 110: 379a. DOI: 10.1016/J.Bpj.2015.11.2046  0.721
2015 Sánchez-Sanz G, Matallanas D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV. MST2-RASSF protein-protein interactions through SARAH domains. Briefings in Bioinformatics. PMID 26443615 DOI: 10.1093/Bib/Bbv070  0.335
2015 Gheorghescu AK, Tywoniuk B, Duess J, Buchete NV, Thompson J. Exposure of chick embryos to cadmium changes the extra-embryonic vascular branching pattern and alters expression of VEGF-A and VEGF-R2. Toxicology and Applied Pharmacology. PMID 26367766 DOI: 10.1016/J.Taap.2015.09.004  0.684
2015 Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, Del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, et al. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. The Journal of Membrane Biology. 248: 611-40. PMID 26063070 DOI: 10.1007/S00232-015-9802-0  0.531
2015 Ryan K, Beirne J, Redmond G, Kilpatrick JI, Guyonnet J, Buchete NV, Kholkin AL, Rodriguez BJ. Nanoscale Piezoelectric Properties of Self-Assembled Fmoc-FF Peptide Fibrous Networks. Acs Applied Materials & Interfaces. 7: 12702-7. PMID 25994251 DOI: 10.1021/Acsami.5B01251  0.315
2015 Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, et al. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chemical Reviews. 115: 3518-63. PMID 25789869 DOI: 10.1021/Cr500638N  0.672
2015 Kelly CM, Muzard J, Brooks BR, Lee GU, Buchete NV. Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules. Physical Chemistry Chemical Physics : Pccp. 17: 9634-43. PMID 25729787 DOI: 10.1039/C4Cp05307A  0.399
2015 Tofoleanu F, Brooks BR, Buchete NV. Modulation of Alzheimer's Aβ protofilament-membrane interactions by lipid headgroups. Acs Chemical Neuroscience. 6: 446-55. PMID 25581460 DOI: 10.1021/Cn500277F  0.377
2015 Kelly CM, Northey T, Ryan K, Brooks BR, Kholkin AL, Rodriguez BJ, Buchete NV. Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field. Biophysical Chemistry. 196: 16-24. PMID 25240398 DOI: 10.1016/J.Bpc.2014.08.009  0.384
2015 Yuan Y, Tywoniuk B, Buchete N. Structural Stability of Diabetes-Related Amylin Protofilaments: Applications to Fibril Design Biophysical Journal. 108: 387a. DOI: 10.1016/J.Bpj.2014.11.2119  0.751
2014 Jambrina PG, Bohuszewicz O, Buchete NV, Kolch W, Rosta E. Molecular mechanisms of asymmetric RAF dimer activation. Biochemical Society Transactions. 42: 784-90. PMID 25109958 DOI: 10.1042/Bst20140025  0.305
2014 Kelly CM, Buchete N. Conformational and Dynamic Properties of Extracellular Domains of Cell Adhesion Molecules Biophysical Journal. 106. DOI: 10.1016/J.Bpj.2013.11.367  0.397
2013 Berezhkovskii AM, Murphy RD, Buchete NV. Note: network random walk model of two-state protein folding: test of the theory. The Journal of Chemical Physics. 138: 036101. PMID 23343306 DOI: 10.1063/1.4776215  0.318
2013 Tofoleanu F, Buchete N. Molecular Interactions of Alzheimer's Aβ Peptide Fibrils and Oligomers with Lipid Membranes Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.3292  0.401
2012 Buchete NV. Unlocking the atomic-level details of amyloid fibril growth through advanced biomolecular simulations. Biophysical Journal. 103: 1411-3. PMID 23062332 DOI: 10.1016/J.Bpj.2012.08.052  0.444
2012 Tofoleanu F, Buchete NV. Alzheimer Aβ peptide interactions with lipid membranes: fibrils, oligomers and polymorphic amyloid channels. Prion. 6: 339-45. PMID 22874669 DOI: 10.4161/Pri.21022  0.416
2012 Murphy RD, Conlon J, Mansoor T, Luca S, Vaiana SM, Buchete NV. Conformational dynamics of human IAPP monomers. Biophysical Chemistry. 167: 1-7. PMID 22609945 DOI: 10.1016/J.Bpc.2012.03.010  0.356
2012 Tofoleanu F, Buchete NV. Molecular interactions of Alzheimer's Aβ protofilaments with lipid membranes. Journal of Molecular Biology. 421: 572-86. PMID 22281438 DOI: 10.1016/J.Jmb.2011.12.063  0.409
2011 Berezhkovskii AM, Tofoleanu F, Buchete NV. Are Peptides Good Two-State Folders? Journal of Chemical Theory and Computation. 7: 2370-2375. PMID 26606612 DOI: 10.1021/Ct200281D  0.383
2011 Buchner GS, Murphy RD, Buchete NV, Kubelka J. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory. Biochimica Et Biophysica Acta. 1814: 1001-20. PMID 20883829 DOI: 10.1016/J.Bbapap.2010.09.013  0.407
2011 Murphy RD, Buchete N. Probing the Kinetic Network of Folding-Unfolding Transitions in Proteins Biophysical Journal. 100: 5-6. DOI: 10.1016/J.Bpj.2010.12.3130  0.419
2009 Rosta E, Buchete NV, Hummer G. Thermostat artifacts in replica exchange molecular dynamics simulations. Journal of Chemical Theory and Computation. 5: 1393-1399. PMID 20046980 DOI: 10.1021/Ct800557H  0.355
2009 Murphy RD, Leahy C, Buchete N. Dynamics of Intra- and Inter-Helix Contact Formation Biophysical Journal. 96. DOI: 10.1016/J.Bpj.2008.12.2186  0.47
2008 Buchete NV, Hummer G. Peptide folding kinetics from replica exchange molecular dynamics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 030902. PMID 18517321 DOI: 10.1103/Physreve.77.030902  0.404
2008 Best RB, Buchete NV, Hummer G. Are current molecular dynamics force fields too helical? Biophysical Journal. 95: L07-9. PMID 18456823 DOI: 10.1529/Biophysj.108.132696  0.35
2008 Buchete NV, Hummer G. Coarse master equations for peptide folding dynamics. The Journal of Physical Chemistry. B. 112: 6057-69. PMID 18232681 DOI: 10.1021/Jp0761665  0.402
2008 Buchete NV, Straub JE, Thirumalai D. Dissecting contact potentials for proteins: relative contributions of individual amino acids. Proteins. 70: 119-30. PMID 17640067 DOI: 10.1002/Prot.21538  0.513
2007 Buchete NV, Hummer G. Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils. Biophysical Journal. 92: 3032-9. PMID 17293399 DOI: 10.1529/Biophysj.106.100404  0.383
2005 Buchete NV, Tycko R, Hummer G. Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments. Journal of Molecular Biology. 353: 804-21. PMID 16213524 DOI: 10.1016/J.Jmb.2005.08.066  0.459
2005 Buchete NV. Book Review: The Art of Molecular Dynamics Simulation Journal of Statistical Physics. 118: 365-367. DOI: 10.1007/S10955-004-8788-2  0.314
2004 Buchete NV, Straub JE, Thirumalai D. Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis. Journal of Molecular Graphics & Modelling. 22: 441-50. PMID 15099839 DOI: 10.1016/J.Jmgm.2003.12.010  0.517
2004 Buchete NV, Straub JE, Thirumalai D. Development of novel statistical potentials for protein fold recognition. Current Opinion in Structural Biology. 14: 225-32. PMID 15093838 DOI: 10.1016/j.sbi.2004.03.002  0.523
2004 Buchete NV, Straub JE, Thirumalai D. Orientational potentials extracted from protein structures improve native fold recognition. Protein Science : a Publication of the Protein Society. 13: 862-74. PMID 15044723 DOI: 10.1110/Ps.03488704  0.597
2004 Buchete NV, Straub JE, Thirumalai D. Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases Polymer. 45: 597-608. DOI: 10.1016/J.Polymer.2003.10.093  0.567
2003 Buchete NV, Straub JE, Thirumalai D. Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures Journal of Chemical Physics. 118: 7658-7671. DOI: 10.1063/1.1561616  0.525
2001 Buchete NV, Straub JE. Mean first-passage time calculations for the coil-to-helix transition: The active helix ising model Journal of Physical Chemistry B. 105: 6684-6697. DOI: 10.1021/Jp0104031  0.485
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