Emmanuel Trizac, Yaakov Levy, and Peter Wolynes Capillarity theory for the fly-casting mechanism, Proc. Natl. Acad. Sci. USA , In press

Tzachi Hagai and Yaakov Levy, Ubiquitin serves not only as a tag, but also assists degradation by inducing protein unfolding, Proc. Natl. Acad. Sci. USA , (2010), 107, 2001-2006

Dana Vuzman, Ariel Azia, and Yaakov Levy, Searching DNA via a "monkey bar" mechanism: the significance of disordered tails, J Mol Biol , (2010), 396, 674-684

Agnes Toth-Petroczy, Istvan Simon, Monika Fuxreiter, Yaakov Levy, Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding, J Amer Chem Soc , (2009), 131, 15084-15085

Ofer Rahat, Uri Alon, Yaakov Levy, and Gideon Schrieber, Understanding Hydrogen-Bond Patterns in Proteins using Network MotifS, Bioinformatics, (2009), 25, 2921-2928

Moshe Ben-David, Orly Noivirt-Birk, Aviv Paz, Jaime Prilusky, Joel L. Sussman and Yaakov Levy, Assessment of CASP8 structure predictions for template free targets, Proteins: Structure, Function, and Bioinformatics, (2009), 77, 50-65

Ariel Azia and Yaakov Levy, Non-native electrostatic interactions can modulate protein folding: Molecular dynamics with a grain of salt, J Mol Biol, (2009), 393, 527-542

Dalit Shental and Yaakov Levy, Folding of glycoproteins: toward understanding the biophysics of the glycosylation code, Current Opinion Structural Biology, (2009), 19, 524-533

Amir Marcovitz and Yaakov Levy, Arc-repressor dimerization on DNA: Folding rate enhancement by colocalization\ , Biophysical J., (2009), 96, 4212-4220

Wei Wang, Wei-Xin Xu, Yaakov Levy, Emmanuel Trizac, and Peter Wolynes, Molecular crowding effects on the kinetics and thermodynamics of protein dimerization, Proc. Natl. Acad. Sci. USA, (2009), 106, 5517-5523

Sam Cho, Yaakov Levy and Peter Wolynes, Quantitative Criteria for Native Energetic Heterogeneity Influences in the Prediction of Protein Folding Kinetics, Proc. Natl. Acad. Sci. USA, (2009), 106, 434-439

Ohad Givaty and Yaakov Levy, Protein sliding along DNA: Dynamics and structural characterization, J. Mol. Biol., (2009), 385, 1087-1098

Amit Mor and Yaakov Levy, Characterization of the unfolded state of repeat proteins, HFSP J., (2008), 2, 405-415

Tzachi Hagai and Yaakov Levy, Folding of Elongated Proteins: Conventional or Anomalous?, J. Amer. Chem. Soc., (2008), 130, 14253-14262,

Dalit Shental-Bechor and Yaakov Levy, Effect of glycosylation on protein folding: A close look at thermodynamic stabilization,Proc. Natl. Acad. Sci. USA, (2008), 105, 8256-8261

Ricardo Broglia, Yaakov Levy, and Guido Tania, HIV-1 Protease folding and the design of drugs which do not create resistance,Curr. Opin. Struct. Biol., (2008), 18, 60-66

Amit Mor, Guy Ziv, and Yaakov Levy, Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats, J. Comp. Chem., (2008), 29, 1992-1998

Yaakov Levy, José N. Onuchic, and Peter G. Wolynes, Fly-casting in protein-DNA binding: Frustration between protein folding and electrostatics facilitates target recognition, Journal of the Amer. Chem. Soc., 129, 738-739, (2007)

Alexander Schug, Paul C. Whitford, Yaakov Levy, and Jose´ N. Onuchic, Mutations as trapdoors to two competing native conformations of the Rop-dimer, Proc. Natl. Acad. Sci. USA, 104, 17674-17679, (2007)   [Article]

Paul C. Whitford, Osamu Miyashita, Yaakov Levy and José N. Onuchic, Conformational transitions of Adenylate Kinase: switching by cracking, J. Mol. Biol., 366, 1661-1671, (2007)

Mingfeng Yang, Boyan Yordanov, Yaakov Levy, Rafael Brischweiler, Shuanghong Huof, Sequence-dependent unfolding pathway plays a critical role in amyloidgenicity of Transthyretin. Biochemistry , 45(39):11992-2002, (2006)   [Pubmed]

Robert Simler, Yaakov Levy, Jose' N. Onuchic, and Robert C. Matthews, The folding energy landscape of the dimerization domain of E. Coli Trp Repressor: A joint experimental and theoretical investigation, J. Mol. Biol., 363(1):262-78, (2006)   [Pubmed]

Yaakov Levy and Jose' N. Onuchic, Energy landscape of protein self-assembly: Lessons from native topology-based models, Proceedings of FCS, (In press), (2006)

Samuel S. Cho, Yaakov Levy, Peter G. Wolynes, p versus q: Structural reaction coordinates capture protein folding on smooth landscapes, Proc. Natl. Acad. Sci. USA, 103, 586-591, (2006)   [Pubmed]

Yaakov Levy and Jose' N. Water mediation in protein folding and molecular recognition, Ann. Rev. Biophys. Biomol. Struct., 35, 389-415, (2006)   [Pubmed]

Yaakov Levy and Jose' N. Onuchic, Mechanism of protein assembly: lessons from minimalist models, Accounts of Chemical Research, 39, 135-142,(2006)   [Pubmed]

Joshua Jortner, Isidore Last, Yaakov Levy, Coulomb instability of multicharged proteins, Int. J Mol. Spec. 249-250, 284-290, (2006)

Yaakov Levy, Isidore Last, and Joshua Jortner, Dynamics of fission and Coulomb explosion of multicharged large finite systems, Mol. Phys. 194, 1227-1234, (2006)

Isidore Last, Yaakov Levy, and Joshua Jortner, Fragmentation channels of large multicharged clusters, J. Chem. Phys. 123, 154301-154312, (2005)   [Pubmed]

Samuel S. Cho, Yaakov Levy, Jose' N. Onuchic, and Peter G. Wolynes, Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation, Phys. Biol., 2, S44-S55 346, (2005)   [Pubmed]

Yaakov Levy, Samuel S. Cho, Jose' N. Onuchic, and Peter G. Wolynes, A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes, J. Mol. Biol., 346, 1121-1145, (2005)   [Pubmed]

Yaakov Levy, Samuel S. Cho, Tongye Shen, Jose' N. Onuchic, and Peter G. Wolynes, Symmetry and frustration in protein energy landscapes: A near degeneracy resolves the Rop dimer-folding mystery, Proc. Natl. Acad. Sci. USA , 102, 2373-2378, (2005)   [Pubmed]

Sichun Yang, Samuel S. Cho, Yaakov Levy , Margaret S. Cheung, Herbert Levine, Peter G. Wolynes and Jose' N. Onuchic, Domain swapping is a consequence of principle of minimal frustration, Proc. Natl. Acad. Sci. USA, 101, 12786-13791, (2004)   [Pubmed]

Yaakov Levy, and Jose' N. Onuchic, Water and proteins: A love-hate relationship, Proc. Natl. Acad. Sci. USA, 101, 3325-3326, (2004)   [Pubmed]

Yaakov Levy, Amedeo Caflisch, Jose' N. Onuchic, and Peter G. Wolynes, The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations, J. Mol. Biol., 340, 67-79, (2004)   [Pubmed]

Yaakov Levy, , Garegin A. Papoian, Jose' N. Onuchic, and Peter G. Wolynes, Energy landscape analysis of protein dimers, Israel J. Chemistry, 44, 281-297, (2004)

Yaakov Levy, Peter G. Wolynes,and Jose' N. Onuchic, Protein topolgy determines binding mechanism, Proc. Natl. Acad. Sci. USA, 101, 511-516, (2004)   [Pubmed]

Florin Despa, Ariel Fernandez, R. Stephen Berry, Yaakov Levy, and Joshua Jortner, Inter-basin motion approach for dynamics of conformationally constrained peptides, J. Chem. Phys., 118, 5673-5682, (2003)

Yaakov Levy and Amedeo Caflisch, The flexibility of monomeric and dimeric HIV-1 protease, J. Phys. Chem. B, 107, 3068-3079, (2003)

Yaakov Levy, , Joshua Jortner, R. Stephen Berry, Eigenvalue spectrum of the master equation for hierarchical dynamics of complex systems, Pysical Chemistry Chemical Physics, 4, 5052-5058, (2002)

Isidore Last, Yaakov Levy, and Joshua Jortner, Beyond the Rayleigh instability limit for multicharged finite systems: from fission to coulomb explosion, Proc. Natl. Acad. Sci. USA, 98, 2188-2193, (2002)   [Pubmed]

Yaakov Levy, and Oren M. Becker, Conformational polymorphism of wild-type and mutant prion proteins: energy landscape analysis, Proteins, 47, 458-468, (2002)   [Pubmed]

Yaakov Levy, Joshua Jortner, and Oren M. Becker, Dynamics of Hierarchical kinetics on the energy landscapes of hexapeptides, J. Chem. Phys. 115, 10533-10547, (2001)

Yaakov Levy, Eilat Hanan, Beka Solomon, and Oren M. Becker, The helix-coil transition of PrP106-126: A molecular dynamic study, Proteins, 45, 382-396, (2001)

Yaakov Levy, Joshua Jortner, and Oren M. Becker, Solvent effects on the energy landscapes and folding kinetics of polyalanines, Proc. Natl. Acad. Sci. USA., 98, 2188-2193, (2001)   [PNAS]

Yaakov Levy and Oren M. Becker, The Transitional Isoform of Wild-Type and Mutant Prion Proteins: Insights from Energy Landscape Analysis, in Conformational Diseases- A Compendium (edited by Beka Solomon, Albert Taraboulos, and Ephraim Katchalski-Katzir 2001)

Yaakov Levy and Oren M. Becker, Energy landscapes of conformationally constrained peptides ,J. Chem. Phys., 114, 993-1009, (2001)

Oren M. Becker, Yaakov Levy, and Orr Ravitz, Flexibility, conformation spaces and the activity of flexible molecules ,J. Phys. Chem. B, 104, 2123-2135, (2000)

Yaakov Levy and Oren M. Becker, Effect of Conformational Constraints on the Topography of Complex Potential Energy Surfaces ,Phys. Rev. Lett 81, 1126-1132, (1998)