Publications


  • Lavi S Bigman and Yaakov Levy, 2018 Entropy-enthalpy compensation in conjugated proteins , Chemical Physics, In Press

  • Yaakov Levy, 2017 On protein assembly and building blocks: Beyond the limits of the LEGO bricks metaphor, Biochemistry, 56: 5040-5048
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  • Goutam Mukherjee, Arumay Pal and Yaakov Levy, 2017 Mechanism of the formation of the RecA–ssDNA nucleoprotein filament structure: a coarse-grained approach, Molecular BioSystems, 13: 2697--2703
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  • Silvia G. Chuartzman, Reinat Nevo, Sharon Waichman, Dalit Shental, Jacob Piehler, Yaakov Levy, Ziv Reich, and Ruti Kapon, 2017 Binding of interferon reduces the force of unfolding for interferon receptor 1, PLOS One, 12(4): e0175413
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  • Yulian Gavrilov, Jessica Leuchter, and Yaakov Levy, 2017 On the Coupling between the Dynamics of Protein and Water, Phys Chem Chem Phys, 19: 8243 - 8257
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  • Dana Krepel and Yaakov Levy, 2017 Intersegmental transfer of proteins between DNA regions in the presence of crowding, Phys Chem Chem Phys, In press

  • Dana Krepel and Yaakov Levy, 2016 Protein diffusion along DNA: On the effect of roadblocks and crowders, Journal of Physics A: Mathematical and Theoretical, 49: 494003
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  • Gad Armony, Etai Jacob, Toot Moran, Yishai Levin, Tevie Mehlman , Yaakov Levy, and Deborah Fass, 2016 Cross-linking Reveals Laminin Coiled-coil Architecture, Proc. Natl. Acad. Sci. USA, 113: 13384-13389
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  • Arnab Bhattacherjee, Dana Krepel and Yaakov Levy, 2016 Coarse-grained models for studying protein diffusion along DNA, WIREs Comput Mol Sci, 6: 515–531
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  • Dana Krepel, David Gomez, Stefan Klumpp, and Yaakov Levy, 2016 Mechanism of facilitated diffusion during DNA search in crowded environments, J Phys Chem B, 120: 11113-11122
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  • Meital Eckshtain-Levi, Eyal Capua, Sivan Refaely-Abramson, Soumyajit Sarkar,Yulian Gavrilov, Shinto Mathew, Yossi Paltiel, Yaakov Levy, Leeor Kronik, Ron Naaman, 2016 “Cold Denaturation” induces inversion of dipole and spin transfer in chiral peptide monolayers, Nature Communicaton, 7: 10744
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  • Yulian Gavrilov, Shlomi Dagan and Yaakov Levy, 2015 Shortening a loop can increase protein native state entropy, PROTEINS: Structure, Function, and Bioinformatics, 83: 2137–2146
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  • Levani Zandarashvili, Alexandre Esadze, Dana Vuzman, Catherine A. Kemme, Yaakov Levy, and Junji Iwahara, 2015 Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble, Proc. Natl. Acad. Sci. USA, 112: E5142 – E5149
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  • Miri Sokolovski, Arnab Bhattacherjee, Naama Kessler, Yaakov Levy and Amnon Horovitz, 2015 Thermodynamic Protein Destabilization by GFP Tagging: A Case of Interdomain Allostery, Biophysical J., 109: 1157-1162
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  • Yulian Gavrilov, Dalit Shental-Bechor, Harry Greenblatt, and Yaakov Levy, 2015 Glycosylation May Reduce Protein Thermodynamic Stability by Inducing a Conformational Distortion, J Phys Chem Lett, 6: 3572-3577
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  • Yulian Gavrilov, Tzachi Hagai, and Yaakov Levy, 2015 Nonspecific yet decisive: Ubiquitination can affect the native-state dynamics of the modified protein, Protein Science, 24: 1580-1592
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  • Sepunaru Lior, Refaely-Abramson Sivan, Lovrincic Robert, Gavrilov Yulian, Agrawal Piyush, Levy Yaakov, Kronik, Leeor, Pecht Israel, Sheves Mordechai, Cahen David, 2015 Electronic Transport via Homo-peptides: The Role of Side Chains and Secondary Structure, J Amer Chem Soc, 137: 9617-9626
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  • Amir Marcovitz, Aviv Naftaly and Yaakov Levy, 2015 Water organization between oppositely charged surfaces: Implications for protein sliding along DNA, J. Chem. Phys., 142: 085102-1 - 10
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  • Garima Mishra and Yaakov Lev, 2015 Molecular determinants of the interactions between proteins and ssDNA, Proc. Natl. Acad. Sci. USA, 112: 5033-5038
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  • Yaakov Levy and Jeffrey Skolnick, 2014 Computational Molecular Biophysics: 40 Years of Achievements, Israel Journal of Chemistry, 54: 1039-1041
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  • Dana Vuzman, 2014 The “Monkey-Bar” Mechanism for Searching for the DNA Target Site: The Molecular Determinants, Israel Journal of Chemistry, 54: 1374-1381
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  • Arnab Bhattacherjee and Yaakov Levy, 2014 Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding, Nucleic Acid Reserach, 42: 12404-12414
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  • Arnab Bhattacherjee and Yaakov Levy, 2014 Search by proteins for their DNA target site: 2. The effect of DNA conformation on the dynamics of multidomain proteins, Nucleic Acid Reserach, 42: 12415-12424
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  • Paul Lawrence, Yulian Gavrilov, Sam Matthews, Minnie I. Langlois, Dalit Shental-Bechor, Harry M. Greenblatt, Brijesh Pandey, Mason Smith, Ryan Paxman, Chad Torgerson, Jacob Merrell, Cameron Ritz, Maxim Prigozhin, Yaakov Levy and Joshua Price, 2014 Criteria for Selecting PEGylation Sites on Proteins for Higher Thermodynamic and Proteolytic Stability, J. Amer. Chem. Soc., 136 (50): 17547–17560
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  • Netaly Khazanov, Amir Marcovitz, Yaakov Levy, 2013 Asymmetric DNA-search dynamics by symmetric dimeric proteins, Biochemistry, 52: 5335-44
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  • Junji Iwahara and Yaakov Levy, 2013 Speed-stability paradox in DNA-scanning by zinc-finger proteins, Transcription, 4: 58-61
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  • Amir Marcovitz and Yaakov Levy, 2013 Weak Frustration Regulates Sliding and Binding Kinetics on Rugged Protein–DNA Landscapes, J Phys Chem B, 117: 13005−13014
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  • Amir Marcovitz and Yaakov Levy, 2013 Obstacles may facilitate and direct DNA search by proteins, Biophysical J, 104: 2042-2050
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  • Shlomi Dagan, Tzachi Hagai, Yulian Gavrilov, Ruti Kapona, Yaakov Levy, Ziv Reich, 2013 Stabilization of a protein conferred by an increase in folded state entropy, Proc. Natl. Acad. Sci. USA, 110: 10628-10633
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  • Berko D, Shental-Bechor D, Cascio P, Levy Y, Admon A,Tirosh B, Goldberg A, Navon A, 2012 The Force needed to unravel the protein terminus determines the direction of translocation into the proteasome, Mol Cell, 48: 601-611
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  • Shental-Bechor D, Smith M, Mackenzie D, Broom A, Marcovitz A, Ghashut F, Go C, Bralha F, Meiering E, Levy Y, 2012 Non-native interactions regulate folding and switching of myristoylated proteins, Proc. Natl. Acad. Sci. USA, 109: 17839-17844
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  • Hagai T, Azia A, Trizac E, Levy Y, 2012 Modulation of folding kinetics of repeat proteins: Interplay between intra- and inter-domain interactions, Biophysical J, 103: 1555-1565
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  • Arviv O, Levy Y, 2012 Folding of multi-domain proteins: Biophysical consequences of tethering even in apparently independent folding, Proteins, 80: 2780-2798
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  • Vuzman D, Levy Y,, 2012 Intrinsically Disordered Regions as Affinity Tuners in Protein-DNA Interactions, Molecular Biosystems, 8: 47-57
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  • Zandarashvili L, Vuzman D, Esadze A, Takayama Y, Sahu D, Levy Y, Iwahara J,, 2012 Asymmetrical Roles of Zinc Fingers in Dynamic DNA-Scanning Process by the Inducible Transcription Factor Egr-1, Proc Nat Acad Sci USA, 109: E1724-E1732
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  • Hagai T, Toth-Petroczy A, Azia A, Levy Y,, 2012 The Origins and Evolution of Ubiquitination Sites, Molecular Biosystems, 8: 1865-1877
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  • Vuzman D, Hoffman Y, Levy Y, 2012 Modulating Protein–DNA Interactions by Post-Translational Modifications at Disordered Regions, Pacific Symposium on Biocomputing, 17: 188-199
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  • Marcovitz A, Levy Y, 2012 Sliding dynamics along DNA: a molecular perspective, "Innovations in Biomolecular Modeling and Simulation", RSC, Biomolecular Sciences, 24, 10: 237-262
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  • Marcovitz A, Levy Y,, 2011 Frustration in Protein-DNA Binding Influences Conformational Switching and Target Search Kinetics, Proc Nat Acad Sci USA, 108: 17957-17962
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  • Hagai T, Azia A, Toth-Petroczy A, Levy Y,, 2011 Intrinsic Disorder in Ubiquitination Substrates, J Mol Biol, 412: 319-324
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  • Shental-Bechor D, Levy Y,, 2011 Communication: Folding of Glycosylated Proteins Under Confinement, J Chem Phys, 135
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  • Fridkin G, Maina T, Nock BA, Blat D, Lev-Goldman V, Scolnik Y, Kapitkovski A, Vachutinsky Y, Shechter Y, Levy Y,, 2011 Intramolecular Azo-Bridge as a Cystine Disulfide Bond Surrogate: Somatostatin-14 and Brain Natriuretic Peptide (Bnp) Analogs, Bioorganic & Medicinal Chemistry, 19: 798-806
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  • Khazanov N, Levy Y,, 2011 Sliding of P53 Along DNA Can be Modulated by Its Oligomeric State and by Cross-Talks Between Its Constituent Domains, J Mol Biol, 408: 335-355
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  • Shental-Bechor D, Arviv O, Hagai T, Levy Y, 2010 Folding of conjugated protein, Ann Rep Comput Chem, 6: 263-277
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  • Vuzman D, Levy Y,, 2010 DNA Search Efficiency is Modulated by Charge Composition and Distribution in the Intrinsically Disordered Tail, Proc Natl Acad Sci USA, 107: 21004-21009
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  • Price JL, Shental-Bechor D, Dhar A, Turner MJ, Powers ET, Gruebele M, Levy Y, Kelly JW,, 2010 Context-Dependent Effects of Asparagine Glycosylation on Pin ww Folding Kinetics and thermodynamics, J Amer Chem Soc, 132: 15359-15367
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  • Vuzman D, Polonsky M, Levy Y,, 2010 Facilitated DNA Search by Multidomain Transcription Factors: Cross Talk Via a Flexible Linker, Biophysical J, 99: 1202-1211
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  • Grossman M, Tworowski D, Dym O, Lee MH, Levy Y, Murphy G, Sagi I,, 2010 The Intrinsic Protein Flexibility of Endogenous Protease Inhibitor Timp-1 Controls Its Binding Interface and Affects Its Function, Biochemistry, 49: 6184-6192
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  • Vuzman D, Azia A, Levy Y,, 2010 Searching DNA Via a "Monkey Bar" Mechanism: the Significance of Disordered Tails, J Mol Biol, 396: 674-684
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  • Trizac E, Levy Y, Wolynes PG,, 2010 Capillarity theory For the Fly-Casting Mechanism, Proc Natl Acad Sci USA, 107: 2746-2750
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  • Hagai T, Levy Y,, 2010 Ubiquitin Not Only Serves as a Tag But Also Assists Degradation by Inducing Protein Unfolding, Proc Natl Acad Sci USA, 107: 2001-2006
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  • Ben-David M, Noivirt-Brik O, Paz A, Prilusky J, Sussman JL, Levy Y,, 2009 Assessment of Casp8 Structure Predictions For Template Free Targets, Proteins-Structure Function and Bioinformatics, 77: 50-65
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  • Toth-Petroczy A, Simon I, Fuxreiter M, Levy Y,, 2009 Disordered Tails of Homeodomains Facilitate DNA Recognition by Providing a Trade-Off Between Folding and Specific Binding, J Amer Chem Soc, 131: 15084-+
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  • Rahat O, Alon U, Levy Y, Schreiber G,, 2009 Understanding Hydrogen-Bond Patterns in Proteins Using Network Motifs, Bioinformatics, 25: 2921-2928
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  • Azia A, Levy Y,, 2009 Nonnative Electrostatic Interactions Can Modulate Protein Folding: Molecular Dynamics With a Grain of Salt, J Mol Biol, 393: 527-542
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  • Shental-Bechor D, Levy Y,, 2009 Folding of Glycoproteins: Toward Understanding the Biophysics of the Glycosylation Code, Curr Opin Struct Biol, 19: 524-533
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  • Marcovitz A, Levy Y,, 2009 Arc-Repressor Dimerization on DNA: Folding Rate Enhancement by Colocalization, Biophysical J, 96: 4212-4220
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  • Wang W, XU WX, Levy Y, Trizac E, Wolynes PG,, 2009 Confinement Effects on the Kinetics and thermodynamics of Protein Dimerization, Proc Natl Acad Sci USA, 106: 5517-5522
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  • Givaty O, Levy Y,, 2009 Protein Sliding Along DNA: Dynamics and Structural Characterization, J Mol Biol, 385: 1087-1097
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  • Whitford PC, Miyashita O, Levy Y, Onuchic JN,, 2007 Conformational Transitions of Adenylate Kinase: Switching by Cracking, J Mol Biol, 366: 1661-1671
  • Schug A, Whitford PC, Levy Y, Onuchic JN,, 2007 Mutations as Trapdoors to Two Competing Native Conformations of the Rop-Dimer, Proc Natl Acad Sci USA, 104: 17674-17679
  • Levy Y, Onuchic JN, Wolynes PG,, 2007 Fly-Casting in Protein-DNA Binding: Frustration Between Protein Folding and Electrostatics Facilitates Target Recognition, J Amer Chem Soc, 129: 738-739

  • Levy Y, Onuchic JN, 2006 Water Mediation in Protein Folding and Molecular Recognition, Annu. Rev. Biophys. Biomol. Struct.: pp 389-415.
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  • Y Levy, J Onuchic, 2006 Mechanisms of Protein Assembly: Lessons from Minimalist Models, Acc Chem Res: pp .135 - 142
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  • Yang M, Yordanov B, Levy Y, Brüschweiler R, Huo S, 2006 Sequence-dependent unfolding pathway plays a critical role in amyloidogenicity of Transthyretin, Biochemistry, 45: 11992-12002
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  • Simler R, Levy Y, Onuchic JN, Matthews RC, 2006 The folding energy landscape of the dimerization domain of E. coli Trp repressor: A joint experimental and theoretical investigation, J Mol Biol, 363: 262-278
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  • Jortner J, Last I, Levy Y, 2006 Coulomb instability of multicharged proteins, Int. J Mol. Spec., 249-250: 284-290
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  • Cho SS, Levy Y, Wolynes PG, 2006 p versus q: Structural reaction coordinates capture protein folding on smooth landscapes, Proc Natl Acad Sci USA, 103: 586-591
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  • Levy Y, Last I, Jortner J, 2006 Dynamic features of fission and coulomb explosion of multicharged large finite system, Mol Phys, 194: 1227-1234
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  • Levy Y , Cho SS , Shen T , Onuchic JN , Wolynes PG, 2005 Symmetry and Frustration in Protein Energy Landscapes: a Near Degeneracy Resolves the Rop Dimer-Folding Mystery, Proc. Natl. Acad. Sci. USA: 2373–2378
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  • Levy Y, Onuchic JN, 2005 Energy Landscapes of Protein Self-Assembly: Lessons from Native Topology-Based Models, Frontiers in Computational Science (FCS 2005): 37-51
  • Last I, Levy Y, Jortner J, 2005 Fragmentation channels of large multicharged clusters: From fission to Coulomb explosion, J Chem Phys, 123: 154301-154312
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  • Cho SS, Levy Y, Onuchic JN, Wolynes PG, 2005 Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation, Phys Biol, 2: S44-S55
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  • Levy Y, Cho SS, Onuchic JN, Wolynes PG, 2005 A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes, J Mol Biol, 346: 1121-1145
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  • Levy Y, Wolynes PG, Onuchic JN, 2004 Protein topology determines binding mechanism, Proc Natl Acad Sci USA, 101: 511-516
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  • Levy Y, Garegin PA, Onuchic JN, Wolynes PG, 2004 Energy landscape analysis of protein dimers, Isr J Chem, 44: 281-297
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  • Levy Y, Onuchic JN, 2004 Water and proteins: A love-hate relationship, Proc Natl Acad Sci USA, 101: 3325-3326
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  • Levy Y, Caflisch A, Onuchic JN, Wolynes PG, 2004 The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations, J Mol Biol, 340: 67-79
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  • Yang S, Cho SS, Levy Y, Cheung MS, Levine H, Wolynes PG, Onuchic JN, 2004 Domain swapping is a consequence of principle of minimal frustration, Proc Natl Acad Sci USA, 101: 13786-13791
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  • Levy Y, Caflisch A, 2003 The flexibility of monomeric and dimeric HIV-1 protease, J Phys Chem B, 107: 3068-3079
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  • Despa F, Fernandez A, Berry RS, Levy Y, Jortner J, 2003 Inter-basin motion approach for dynamics of conformationally constrained peptides, J Chem Phys, 118: 5673-5682
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  • Levy Y, Jortner J, Berry RS, 2002 Eigenvalue spectrum of the master equation for hierarchical dynamics of complex systems, Phys Chem Chem Phys, 4: 5052-5058
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  • Levy Y, Becker OM, 2002 Conformational polymorphism of wild-type and mutant prion proteins: energy landscape analysis, Proteins, 47: 458-468
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  • Last I, Levy Y, Jortner J, 2002 Beyond the Rayleigh instability limit for multicharged finite systems: from fission to coulomb explosion, Proc Natl Acad Sci USA, 98: 9107-9122
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  • Levani Zandarashvili, Alexandre Esadze, Dana Vuzman, Catherine A. Kemme, Yaakov Levy, and Junji Iwahara, 2001 Balancing between affinity and speed in target DNA search Q:4; 5; 6; 7 by zinc-finger proteins via modulation of dynamic conformational ensemble, Proc. Natl. Acad. Sci. USA: In Press
  • Levani Zandarashvili, Alexandre Esadze, Dana Vuzman, Catherine A. Kemme, Yaakov Levy, and Junji Iwahara, 2001 Balancing between affinity and speed in target DNA search Q:4; 5; 6; 7 by zinc-finger proteins via modulation of dynamic conformational ensemble, Proc. Natl. Acad. Sci. USA: In Press
  • Levy Y, Becker OM, 2001 The Transitional Isoform of Wild-Type and Mutant Prion Proteins: Insights from Energy Landscape Analysis, in Conformational Diseases- A Compendium
  • Levy Y, Jortner J, Becker OM, 2001 Solvent effects on the energy landscapes and folding kinetics of polyalanines, Proc Natl Acad Sci USA, 98: 2188-2193
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  • Levy Y, Hanan E, Solomon B, Becker OM, 2001 The helix-coil transition of PrP106-126: A molecular dynamic study, Proteins, 45: 382-396
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  • Levy Y, Becker OM, 2001 Energy landscapes of conformationally constrained peptides, J Chem Phys, 114: 993-1009
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  • Levy Y, Jortner J, Becker OM, 2001 Dynamics of Hierarchical kinetics on the energy landscapes of hexapeptides, J Chem Phys, 115: 10533-10547
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  • Becker OM, Levy Y, Ravitz O, 2000 Flexibility, conformation spaces and the activity of flexible molecules, J Phys Chem B, 104: 2123-2135
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  • Levy Y, Becker OM, 1998 Effect of Conformational Constraints on the Topography of Complex Potential Energy Surfaces, Phys Rev Lett, 81: 1126-1132
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