José N Onuchic

发表

The role of coevolutionary signatures in protein interaction dynamics, complex inference, molecular recognition, and mutational landscapes.

Faruck Morcos, José N Onuchic, F. Morcos, 2019, Current opinion in structural biology.

Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

Peter G Wolynes, Mingchen Chen, Xingcheng Lin, 2016, The journal of physical chemistry. B.

From structure to function: the convergence of structure based models and co-evolutionary information.

Faruck Morcos, José N Onuchic, Biman Jana, 2014, Physical chemistry chemical physics : PCCP.

Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields.

Peter G Wolynes, Wei Lu, Mingchen Chen, 2018, Journal of chemical theory and computation.

Folding a protein in the computer: reality or hope?

José N Onuchic, Angel E Garcia, 2005, Structure.

Role of metabolic spatiotemporal dynamics in regulating biofilm colony expansion

Mingyang Lu, José N Onuchic, Federico Bocci, 2018, Proceedings of the National Academy of Sciences.

Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function.

Alexander Schug, José N Onuchic, Paul C Whitford, 2009, Biophysical journal.

Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.

Wei Lu, Peter G Wolynes, Mingchen Chen, 2017, The journal of physical chemistry. B.

Jamming proteins with slipknots and their free energy landscape.

José N Onuchic, Piotr Sułkowski, Joanna I Sułkowska, 2009, Physical review letters.

Transferable model for chromosome architecture

Peter G Wolynes, Erez Lieberman Aiden, José N Onuchic, 2016, Proceedings of the National Academy of Sciences.

A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes.

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2005, Journal of molecular biology.

A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory.

José N Onuchic, J. Onuchic, M. Cheung, 2004, Biophysical journal.

Simple energy landscape model for the kinetics of functional transitions in proteins.

Osamu Miyashita, Peter G Wolynes, José N Onuchic, 2005, The journal of physical chemistry. B.

Jagged–Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype

Cecilia Clementi, Eshel Ben-Jacob, Mingyang Lu, 2015, Proceedings of the National Academy of Sciences.

Constructing sequence‐dependent protein models using coevolutionary information

Mohit Raghunathan, José N Onuchic, Jeffrey K Noel, 2016, Protein science : a publication of the Protein Society.

Elucidating the druggable interface of protein−protein interactions using fragment docking and coevolutionary analysis

Faruck Morcos, José N Onuchic, Hualiang Jiang, 2016, Proceedings of the National Academy of Sciences.

Probing the kinetics of single molecule protein folding.

José N Onuchic, George Stell, Vitor B P Leite, 2004, Biophysical journal.

Mirror images as naturally competing conformations in protein folding.

Wolfgang Wenzel, Alexander Schug, José N Onuchic, 2012, The journal of physical chemistry. B.

Free energy landscape for the binding process of Huperzine A to acetylcholinesterase

Jing Chen, Jianpeng Ma, Hualiang Jiang, 2013, Proceedings of the National Academy of Sciences.

A semi-analytical description of protein folding that incorporates detailed geometrical information.

José N Onuchic, Jeffrey K Noel, J. Onuchic, 2011, The Journal of chemical physics.

Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2005, Physical biology.

Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates.

Cecilia Clementi, José N Onuchic, Leslie L. Chavez, 2004, Journal of the American Chemical Society.

Mutations as trapdoors to two competing native conformations of the Rop-dimer

Yaakov Levy, Alexander Schug, José N Onuchic, 2007, Proceedings of the National Academy of Sciences.

Modeling putative therapeutic implications of exosome exchange between tumor and immune cells

Eshel Ben-Jacob, Mingyang Lu, José N Onuchic, 2014, Proceedings of the National Academy of Sciences.

Knotting pathways in proteins.

José N Onuchic, Jeffrey K Noel, Joanna I Sułkowska, 2013, Biochemical Society transactions.

Protein topology determines binding mechanism.

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Kinesin's backsteps under mechanical load.

Changbong Hyeon, José N Onuchic, Stefan Klumpp, 2009, Physical chemistry chemical physics : PCCP.

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

Peter G Wolynes, Nicholas P Schafer, Faruck Morcos, 2014, Proceedings of the National Academy of Sciences.

Geometrical features of the protein folding mechanism are a robust property of the energy landscape: a detailed investigation of several reduced models.

Alexander Schug, José N Onuchic, J. Onuchic, 2008, The journal of physical chemistry. B.

The native energy landscape for interleukin-1beta. Modulation of the population ensemble through native-state topology.

José N Onuchic, Leslie L. Chavez, J. Onuchic, 2005, Journal of molecular biology.

Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.

José N Onuchic, Karissa Y Sanbonmatsu, Paul C Whitford, 2010, RNA.

Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches.

José N Onuchic, Karissa Y Sanbonmatsu, Jeffrey K Noel, 2014, Biophysical journal.

Direct coupling analysis for protein contact prediction.

Terence Hwa, Martin Weigt, Faruck Morcos, 2014, Methods in molecular biology.

Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery.

Peter G Wolynes, Tongye Shen, Yaakov Levy, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch.

José N Onuchic, Karissa Y Sanbonmatsu, Jeffrey K Noel, 2012, Journal of the American Chemical Society.

From protein folding to protein function and biomolecular binding by energy landscape theory.

Alexander Schug, José N Onuchic, J. Onuchic, 2010, Current opinion in pharmacology.

The dual-basin landscape in GFP folding

José N Onuchic, Shachi Gosavi, J. Onuchic, 2008, Proceedings of the National Academy of Sciences.

Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model.

José N Onuchic, Charles L Brooks, J. Onuchic, 2004, Journal of molecular biology.

Internal strain regulates the nucleotide binding site of the kinesin leading head

Changbong Hyeon, José N Onuchic, J. Onuchic, 2007, Proceedings of the National Academy of Sciences.

Conformational Transitions in Adenylate Kinase

José N Onuchic, Paul C Whitford, Shachi Gosavi, 2008, Journal of Biological Chemistry.

Conformational transitions of adenylate kinase: switching by cracking.

Osamu Miyashita, Yaakov Levy, José N Onuchic, 2007, Journal of molecular biology.

Mechanical control of the directional stepping dynamics of the kinesin motor

Changbong Hyeon, José N Onuchic, J. Onuchic, 2007, Proceedings of the National Academy of Sciences.

Modeling the Genetic Regulation of Cancer Metabolism: Interplay between Glycolysis and Oxidative Phosphorylation.

Jianpeng Ma, Eshel Ben-Jacob, Mingyang Lu, 2017, Cancer research.

Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins.

José N Onuchic, Joanna I Sulkowska, J. Onuchic, 2013, The journal of physical chemistry letters.

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.

José N Onuchic, Karissa Y Sanbonmatsu, Jeffrey K Noel, 2015, Physical review letters.

The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.

José N Onuchic, Jeffrey K Noel, Paul C Whitford, 2012, The journal of physical chemistry. B.

The folding energy landscape of the dimerization domain of Escherichia coli Trp repressor: a joint experimental and theoretical investigation.

Yaakov Levy, José N Onuchic, J. Onuchic, 2006, Journal of molecular biology.

Backtracking on the folding landscape of the β-trefoil protein interleukin-1β?

José N Onuchic, J. Onuchic, M. Roy, 2008, Proceedings of the National Academy of Sciences.

A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins

José N Onuchic, J. Onuchic, A. F. Pereira De Araújo, 2009, Proceedings of the National Academy of Sciences.

Effective stochastic dynamics on a protein folding energy landscape.

Herbert Levine, José N Onuchic, Sichun Yang, 2006, The Journal of chemical physics.

Extracting function from a β-trefoil folding motif

José N Onuchic, Paul C Whitford, Shachi Gosavi, 2008, Proceedings of the National Academy of Sciences.

High-resolution protein complexes from integrating genomic information with molecular simulation

Terence Hwa, Martin Weigt, Alexander Schug, 2009, Proceedings of the National Academy of Sciences.

Strand swapping regulates the iron-sulfur cluster in the diabetes drug target mitoNEET

José N Onuchic, J. Onuchic, P. Jennings, 2012, Proceedings of the National Academy of Sciences.

Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition.

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2007, Journal of the American Chemical Society.

Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration.

Herbert Levine, José N Onuchic, Sichun Yang, 2005, Journal of molecular biology.

Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center.

Osamu Miyashita, José N Onuchic, J. Onuchic, 2004, Proceedings of the National Academy of Sciences of the United States of America.

β-Bulge triggers route-switching on the functional landscape of interleukin-1β

José N Onuchic, Shachi Gosavi, J. Onuchic, 2012, Proceedings of the National Academy of Sciences.

Water and proteins: a love-hate relationship.

Yaakov Levy, José N Onuchic, J. Onuchic, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Slipknotting upon native-like loop formation in a trefoil knot protein

José N Onuchic, Jeffrey K Noel, Joanna I Sułkowska, 2010, Proceedings of the National Academy of Sciences.