J. Onuchic

发表

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

C. Sander, R. Zecchina, F. Morcos, 2011, Proceedings of the National Academy of Sciences.

Genomics-aided structure prediction

F. Morcos, J. Onuchic, T. Hwa, 2012, Proceedings of the National Academy of Sciences.

Funnels, pathways, and the energy landscape of protein folding: A synthesis

J. Onuchic, N. Socci, P. Wolynes, 1994, Proteins.

Protein folding funnels: the nature of the transition state ensemble.

J. Onuchic, N. Socci, P. Wolynes, 1996, Folding & design.

Toward an outline of the topography of a realistic protein-folding funnel.

J. Onuchic, N. Socci, P. Wolynes, 1995, Proceedings of the National Academy of Sciences of the United States of America.

A Molecular Shift Register Based on Electron Transfer

J. Hopfield, J. Onuchic, D. Beratan, 1988, Science.

Navigating the folding routes

J. Onuchic, P. Wolynes, D. Thirumalai, 1995, Science.

Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes

F. Morcos, J. Onuchic, R. R. Cheng, 2016, Molecular Biology and Evolution.

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

J. Onuchic, A. Garcia, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Protein folding funnels: a kinetic approach to the sequence-structure relationship.

J. Onuchic, P. Leopold, M. Montal, 1992, Proceedings of the National Academy of Sciences of the United States of America.

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

J. Onuchic, P. Wolynes, S. Takada, 2006, Proceedings of the National Academy of Sciences.

Understanding protein folding with energy landscape theory Part I: Basic concepts

J. Onuchic, S. Plotkin, 2002, Quarterly Reviews of Biophysics.

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

J. Onuchic, H. Nymeyer, C. Clementi, 2000, Journal of molecular biology.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

Steven P. Callahan, Jocelyn Y. Kishi, Neva C. Durand, 2018, bioRxiv.

Understanding stochastic simulations of the smallest genetic networks.

J. Onuchic, P. Wolynes, D. Schultz, 2007, The Journal of chemical physics.

Self-regulating gene: an exact solution.

J. Onuchic, P. Wolynes, A. Walczak, 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

Theory of Protein Folding This Review Comes from a Themed Issue on Folding and Binding Edited Basic Concepts Perfect Funnel Landscapes and Common Features of Folding Mechanisms

J. Onuchic, P. Wolynes, José Nelson Onuchic, 2022 .

An all‐atom structure‐based potential for proteins: Bridging minimal models with all‐atom empirical forcefields

J. Onuchic, A. Schug, J. Noel, 2009, Proteins.

Robustness and generalization of structure‐based models for protein folding and function

J. Onuchic, A. Schug, H. Lammert, 2009, Proteins.

Protein Structure Prediction in CASP13 using AWSEM-Suite.

Wei Lu, Xun Chen, Peter G Wolynes, 2020, Journal of chemical theory and computation.

Allostery in the ferredoxin protein motif does not involve a conformational switch

Heiko Lammert, José N. Onuchic, Paul C. Whitford, 2011, Proceedings of the National Academy of Sciences.

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

J. Onuchic, P. Wolynes, O. Miyashita, 2003, Proceedings of the National Academy of Sciences of the United States of America.

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.

Theory of protein folding: the energy landscape perspective.

J. Onuchic, P. Wolynes, Z. Luthey-Schulten, 1997, Annual review of physical chemistry.

Protein folding mechanisms and the multidimensional folding funnel

P G Wolynes, J. Onuchic, N. Socci, 1998, Proteins.

Taking a Walk on a Landscape

C L Brooks, J. Onuchic, D. Wales, 2001, Science.

Conformational transitions of adenylate kinase: switching by cracking.

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

Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level

Nicholas P. Schafer, G. Rangarajan, J. Onuchic, 2019, Biomolecules.

PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer

Nicholas P. Schafer, G. Rangarajan, J. Onuchic, 2018, bioRxiv.

PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer

G. Rangarajan, J. Onuchic, A. Grishaev, 2018, bioRxiv.

Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics

F. Morcos, J. Onuchic, J. Noel, 2016, F1000Research.

Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.

C L Brooks, J. Onuchic, C. Brooks, 1999, Proceedings of the National Academy of Sciences of the United States of America.

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.

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.

The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations.

Peter G Wolynes, Amedeo Caflisch, Yaakov Levy, 2004, Journal of molecular biology.

Energy Landscape Analysis of Protein Dimers

Peter G. Wolynes, José N. Onuchic, Yaakov Levy, 2004 .

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.

Proteins at Work

José N. Onuchic, Paul C. Whitford, Michael A. Jamros, 2010, The Journal of Biological Chemistry.

Ligand-induced global transitions in the catalytic domain of protein kinase A

J. Onuchic, P. Jennings, Changbong Hyeon, 2009, Proceedings of the National Academy of Sciences.

Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes

F. Morcos, J. Onuchic, R. R. Cheng, 2016, bioRxiv.

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

José N. Onuchic, Herbert Levine, Faruck Morcos, 2014, Proceedings of the National Academy of Sciences.

Turning Oscillations Into Opportunities: Lessons from a Bacterial Decision Gate

Eshel Ben-Jacob, Daniel Schultz, Mingyang Lu, 2013, Scientific Reports.

Structure-function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease.

F. Morcos, J. Onuchic, P. Jennings, 2015, Biochimica et biophysica acta.

Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill

Jianpeng Ma, Jeffrey K. Noel, José N. Onuchic, 2018, Proceedings of the National Academy of Sciences.

Order and disorder control the functional rearrangement of influenza hemagglutinin

J. Onuchic, Jianpeng Ma, J. Noel, 2014, Proceedings of the National Academy of Sciences.

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.

Protein electron transfer rates set by the bridging secondary and tertiary structure.

J. Onuchic, D. Beratan, J. Betts, 1991, Science.

Transferable model for chromosome architecture

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

Domain swapping is a consequence of minimal frustration.

Samuel S. Cho, J. Onuchic, P. Wolynes, 2004, Proceedings of the National Academy of Sciences of the United States of America.

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.

Water mediation in protein folding and molecular recognition.

J. Onuchic, Y. Levy, 2006, Annual review of biophysics and biomolecular structure.

The energy landscape for protein folding and possible connections to function

Margaret S. Cheung, José N. Onuchic, Leslie L. Chavez, 2004 .

Probing the kinetics of single molecule protein folding.

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

DIFFUSIVE DYNAMICS OF THE REACTION COORDINATE FOR PROTEIN FOLDING FUNNELS

J. Onuchic, N. Socci, P. Wolynes, 1996, cond-mat/9601091.

Pressure-induced protein-folding/unfolding kinetics.

J. Onuchic, A. E. García, N. Hillson, 1999, Proceedings of the National Academy of Sciences of the United States of America.

The energy landscape theory of protein folding: insights into folding mechanisms and scenarios.

J. Onuchic, N. Socci, H. Nymeyer, 2000, Advances in protein chemistry.

How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta.

J. Onuchic, P. Jennings, C. Clementi, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration.

J. Onuchic, N. Socci, H. Nymeyer, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse

J. Onuchic, A. Garcia, M. Cheung, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Mirror images as naturally competing conformations in protein folding.

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

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.

The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding.

J. Onuchic, P. Whitford, V. Leite, 2010, Biophysical journal.

Direct single-molecule observation of a protein living in two opposed native structures

Jason J. Lavinder, J. Onuchic, A. Schug, 2009, 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.

Folding time predictions from all-atom replica exchange simulations.

J. Onuchic, H. Levine, A. Garcia, 2007, Journal of molecular biology.

Effective stochastic dynamics on a protein folding energy landscape.

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

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.

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.

Folding funnels and frustration in off-lattice minimalist protein landscapes.

J. Onuchic, H. Nymeyer, A. Garcia, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L.

J. Onuchic, A. Garcia, C. Clementi, 2003, Journal of molecular biology.

Prediction of folding mechanism for circular-permuted proteins.

J. Onuchic, P. Jennings, C. Clementi, 2001, Journal of molecular biology.

Probing the folding free energy landscape of the src-SH3 protein domain

Joan-Emma Shea, Charles L Brooks, J. Onuchic, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Solvation in protein folding analysis: combination of theoretical and experimental approaches.

M Wilmanns, L Serrano, J. Onuchic, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

J. Onuchic, A. Schug, Serdal Kirmizialtin, 2015, Methods in enzymology.

Absolute rate theories of epigenetic stability.

J. Onuchic, P. Wolynes, A. Walczak, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Extinction and resurrection in gene networks

J. Onuchic, P. Wolynes, A. Walczak, 2008, Proceedings of the National Academy of Sciences.

Molecular level stochastic model for competence cycles in Bacillus subtilis

J. Onuchic, P. Wolynes, D. Schultz, 2007, Proceedings of the National Academy of Sciences.

Biomolecular dynamics: order–disorder transitions and energy landscapes

J. Onuchic, P. Whitford, K. Sanbonmatsu, 2012, Reports on progress in physics. Physical Society.

Classical and quantum pictures of reaction dynamics in condensed matter: resonances, dephasing, and all that

J. Onuchic, P. Wolynes, 1988 .

Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation

J. Onuchic, H. Levine, Mingyang Lu, 2020, Journal of the Royal Society Interface.

Intercellular stress reconstitution from traction force data.

J. Onuchic, W. Rappel, H. Levine, 2014, Biophysical journal.

Dimeric interactions and complex formation using direct coevolutionary couplings

Ricardo N Dos Santos, F. Morcos, J. Onuchic, 2015, Scientific Reports.

The Energetics and Physiological Impact of Cohesin Extrusion

Neva C. Durand, Erez Lieberman Aiden, Michele Di Pierro, 2018, Cell.

A structural perspective on the dynamics of kinesin motors.

J. Onuchic, Changbong Hyeon, 2011, Biophysical journal.

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

Erez Lieberman Aiden, Michele Di Pierro, J. Onuchic, 2017, Proceedings of the National Academy of Sciences.

Investigation of routes and funnels in protein folding by free energy functional methods.

J. Onuchic, S. Plotkin, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Understanding protein folding with energy landscape theory Part II: Quantitative aspects

J. Onuchic, S. Plotkin, 2002, Quarterly Reviews of Biophysics.

Folding kinetics of proteinlike heteropolymers

J. Onuchic, N. Socci, 1994, cond-mat/9404001.

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding

J. Onuchic, E. Wang, P. Whitford, 2012, Proceedings of the National Academy of Sciences.

Topological frustration and the folding of interleukin-1 beta.

Leslie L. Chavez, J. Onuchic, P. Jennings, 2006, Journal of molecular biology.

Effect of friction on electron transfer in biomolecules

J. Onuchic, V. Ambegaokar, A. Garg, 1985 .

Tristability in cancer-associated microRNA-TF chimera toggle switch.

E. Ben-Jacob, J. Onuchic, M. Jolly, 2013, The journal of physical chemistry. B.

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.

Dodging the crisis of folding proteins with knots

Piotr Sułkowski, José Onuchic, Joanna I Sułkowska, 2009, Proceedings of the National Academy of Sciences.

Toward decoding the principles of cancer metastasis circuits.

Eshel Ben-Jacob, Mingyang Lu, Mohit Kumar Jolly, 2014, Cancer research.

The three-way switch operation of Rac1/RhoA GTPase-based circuit controlling amoeboid-hybrid-mesenchymal transition

Eshel Ben-Jacob, Mingyang Lu, Bin Huang, 2014, Scientific Reports.

Operating principles of Notch–Delta–Jagged module of cell–cell communication

Cecilia Clementi, Eshel Ben-Jacob, José N. Onuchic, 2015 .

MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination

Eshel Ben-Jacob, José N. Onuchic, Mingyang Lu, 2013, Proceedings of the National Academy of Sciences.

Quantifying Cancer Epithelial-Mesenchymal Plasticity and its Association with Stemness and Immune Response

J. Onuchic, H. Levine, Federico Bocci, 2019, Journal of clinical medicine.

Testing the gene expression classification of the EMT spectrum.

Jason T. George, J. Onuchic, S. Hanash, 2019, Physical biology.

Protein electron transport: single versus multiple pathways

José N. Onuchic, David N. Beratan, J. Onuchic, 1993 .

Understanding the Principles of Pattern Formation Driven by Notch Signaling by Integrating Experiments and Theoretical Models

J. Onuchic, Federico Bocci, M. Jolly, 2020, Frontiers in Physiology.

Coevolutionary signals across protein lineages help capture multiple protein conformations

Terence Hwa, José N. Onuchic, Faruck Morcos, 2013, 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.

Theory and Practice of Electron Transfer within Proteinminus signProtein Complexes: Application to the Multidomain Binding of Cytochrome c by Cytochrome c Peroxidase.

J. Onuchic, D. Beratan, B. Hoffman, 1996, Chemical reviews.

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.

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

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.

Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks.

J. Onuchic, H. Levine, Federico Bocci, 2019, Methods in molecular biology.

An approach to detect the dominant folds of proteinlike heteropolymers from the statistics of a homopolymeric chain

J. Onuchic, P. Wolynes, E. Nelson, 2000 .

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.

Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis

Eshel Ben-Jacob, José N. Onuchic, Mingyang Lu, 2015, Front. Oncol..

De Novo Prediction of Human Chromosome Structures: Epigenetic Marking Patterns Encode Genome Architecture

Michele Di Pierro, J. Onuchic, P. Wolynes, 2017, bioRxiv.

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.

Jamming proteins with slipknots and their free energy landscape.

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

Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape.

J. Onuchic, J. Finke, 2005, Biophysical journal.

Drug-Tolerant Idling Melanoma Cells Exhibit Theory-Predicted Metabolic Low-Low Phenotype

Corey E. Hayford, Keisha N. Hardeman, J. Onuchic, 2020, Frontiers in Oncology.

Drug-Tolerant Idling Melanoma Cells Exhibit Theory-Predicted Metabolic Low-Low Phenotype

Corey E. Hayford, Keisha N. Hardeman, J. Onuchic, 2019, bioRxiv.

Statistical Physics of Macromolecules

J. Onuchic, A. Grosberg, A. Khokhlov, 1995 .

Interrogating the Topological Robustness of Gene Regulatory Circuits

E. Ben-Jacob, J. Onuchic, H. Levine, 2016, bioRxiv.

Exploring chromosomal structural heterogeneity across multiple cell lines

Vinícius G. Contessoto, J. Onuchic, P. Wolynes, 2020, eLife.

The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome

Vinícius G. Contessoto, Matheus F Mello, J. Onuchic, 2020, Nucleic acids research.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

Steven P. Callahan, Jocelyn Y. Kishi, Neva C. Durand, 2018, bioRxiv.

Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes

Davit A. Potoyan, J. Onuchic, P. Wolynes, 2018, Proceedings of the National Academy of Sciences.

Title : De Novo Prediction of Human Chromosome Structure s : Epigenetic Marking Patterns Encode Genome Architecture

Erez Lieberman Aiden, Michele Di Pierro, J. Onuchic, 2017 .

Uncovering the molecular mechanisms behind disease-associated leptin variants

Nicholas P. Schafer, J. Onuchic, N. Schafer, 2018, The Journal of Biological Chemistry.

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.

Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes

J. Onuchic, A. F. Pereira De Araújo, M. G. Van der Linden, 2016, Proteins.

Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure

J. Onuchic, A. F. Pereira De Araújo, L. C. Oliveira, 2014, Proteins.

Electron tunneling pathways in proteins: influences on the transfer rate

J. Onuchic, D. Beratan, 1989, Photosynthesis Research.

A method to analyze multi-pathway effects on protein mediated donor-acceptor coupling interactions

J. Onuchic, D. Beratan, S. Skourtis, 1996 .

Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins

P. Beroza, J. Onuchic, D. Beratan, 1995, Journal of bioenergetics and biomembranes.

Effective two-state systems in bridge-mediated electron transfer. A Green function analysis

J. Onuchic, S. Skourtis, 1993 .

Long‐Range Electron Transfer in Myoblobin a

J. Onuchic, H. Gray, D. Beratan, 1988, Annals of the New York Academy of Sciences.

Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures.

J. Onuchic, A. Schug, J. Noel, 2015, The Journal of chemical physics.

Conservation of complex knotting and slipknotting patterns in proteins

Eric J. Rawdon, Joanna I Sułkowska, J. Onuchic, 2012, Proceedings of the National Academy of Sciences.

Limiting forms of the tunneling matrix element in the long distance bridge mediated electron transfer problem

J. Hopfield, J. Onuchic, D. Beratan, 1985 .

Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function

José N. Onuchic, Paul C. Whitford, Michael A. Jamros, 2012, PLoS Comput. Biol..

The pierced lasso topology leptin has a bolt on dynamic domain composed by the disordered loops I and III.

J. Onuchic, J. Noel, P. Jennings, 2020, Journal of molecular biology.

Electronic shift register memory based on molecular electron-transfer reactions

J. Hopfield, J. Onuchic, D. Beratan, 1989 .

Design of a True Molecular Electronic Device: The Electron Transfer Shift Register Memory

John J. Hopfield, José N. Onuchic, David N. Beratan, 1989 .

Electron tunneling through covalent and noncovalent pathways in proteins

John J. Hopfield, José N. Onuchic, David N. Beratan, 1987 .

Generalized pathway model to compute and analyze tunneling matrix elements in proteins

J. Onuchic, P. C. P. Andrade, 1998 .

Electron Transfer in Proteins: Beyond the Single Pathway Approach.

J. Onuchic, J. Regan, 1996 .

A Tubular View of Electron Transfer in Azurin

J. Onuchic, J. Regan, 1996 .

Electron-tunneling pathways in proteins.

J. Onuchic, H. Gray, D. Beratan, 1992, Science.

Tunneling Pathways In Proteins: From Biology To Molecular Electronics

J. Onuchic, D. Beratan, 1990, [1990] Proceedings of the Twelfth Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

A NEW FRAMEWORK FOR ELECTRON-TRANSFER CALCULATIONS-BEYOND THE PATHWAYS-LIKE MODELS

J. Onuchic, I. Balabin, 1998 .

Pericytes enable effective angiogenesis in the presence of proinflammatory signals

J. Onuchic, A. Levchenko, H. Levine, 2019, Proceedings of the National Academy of Sciences.

Pericytes enable effective angiogenesis in the presence of pro-inflammatory signals

J. Onuchic, A. Levchenko, H. Levine, 2019, bioRxiv.

Deciphering the Dynamics of Epithelial-Mesenchymal Transition and Cancer Stem Cells in Tumor Progression

J. Onuchic, H. Levine, Federico Bocci, 2018, Current Stem Cell Reports.

A biophysical model uncovers the size distribution of migrating cell clusters across cancer types.

J. Onuchic, Federico Bocci, Mohit Kumar Jolly, 2019, Cancer research.

A biophysical model uncovers the size distribution of migrating cell clusters across cancer types

J. Onuchic, Federico Bocci, M. Jolly, 2019, bioRxiv.

A biophysical model uncovers the size distribution of migrating cell clusters across cancer types

J. Onuchic, Federico Bocci, M. Jolly, 2019, bioRxiv.

BAP1 forms a trimer with HMGB1 and HDAC1 that modulates gene × environment interaction with asbestos

J. Onuchic, S. Pastorino, H. Pass, 2021, Proceedings of the National Academy of Sciences.

The folding funnel landscape for the peptide met‐enkephalin

U H Hansmann, Y Okamoto, Y. Okamoto, 1998, Proteins.

Turning death into creative force during biofilm engineering

E. Ben-Jacob, J. Onuchic, D. Schultz, 2012, Proceedings of the National Academy of Sciences.

Elucidating cancer metabolic plasticity by coupling gene regulation with metabolic pathways

J. Onuchic, H. Levine, Mingyang Lu, 2019, Proceedings of the National Academy of Sciences.

Towards Decoding the Metabolic Plasticity in Cancer: Coupling of Gene Regulation and Metabolic Pathways

J. Onuchic, H. Levine, Mingyang Lu, 2018, bioRxiv.

Structure of the human monomeric NEET protein MiNT and its role in regulating iron and reactive oxygen species in cancer cells

J. Onuchic, P. Jennings, R. Mittler, 2017, Proceedings of the National Academy of Sciences.

Dynamic views of ribosome function: Energy landscapes and ensembles

James B. Munro, Daniel S. Terry, J. Onuchic, 2011 .

Classification : Biological Sciences Molecular Origin of the Weak Susceptibility of Kinesin Velocity to Loads and its Relation to the Collective Behavior of Kinesins Short title : Molecular Origin of the Weak Susceptibility of Kinesin

J. Onuchic, A. Kolomeisky, Q. Wang, 2017 .

Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein

J. Onuchic, P. Jennings, R. Mittler, 2011, Proceedings of the National Academy of Sciences.

Structural consequences of hereditary spastic paraplegia disease-related mutations in kinesin

J. Onuchic, M. Diehl, B. Jana, 2018, Proceedings of the National Academy of Sciences.

NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype

Jason T. George, J. Onuchic, S. Hanash, 2018, bioRxiv.

Testing the gene expression classification of the EMT spectrum

Jason T. George, J. Onuchic, S. Hanash, 2018, bioRxiv.

Numb prevents a complete EMT by modulating Notch signalling

J. Onuchic, S. Hanash, H. Levine, 2017, bioRxiv.

Numb prevents a complete epithelial–mesenchymal transition by modulating Notch signalling

J. Onuchic, S. Hanash, H. Levine, 2017, Journal of The Royal Society Interface.

Rapid assessment of T-cell receptor specificity of the immune repertoire

Nicholas P. Schafer, Jason T. George, J. Onuchic, 2020, Nature Computational Science.

What protein folding teaches us about biological function and molecular machines.

J. Onuchic, P. Whitford, 2015, Current opinion in structural biology.

Key aspects of the past 30 years of protein design

J. Onuchic, I. Coluzza, V. Bianco, 2022, Reports on progress in physics. Physical Society.

Theory and Practice of Electron Transfer Within Protein-Protein Complexes: Application to the Multidomain Binding of Cytochrome c by Cytochrome c Peroxidase

J. Onuchic, D. Beratan, B. Hoffman, 1997 .

Electron tunneling in azurin: the coupling across a β-sheet

J. Onuchic, H. Gray, L. Skov, 1995 .

Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry

Michael L. Wang, J. Onuchic, X. Shu, 2019, Nature Communications.

A driving and coupling “Pac-Man” mechanism for chromosome poleward translocation in anaphase A

J. Onuchic, Jian Liu, 2006, Proceedings of the National Academy of Sciences.

Exploring the energy landscape of riboswitches using collective variables based on tertiary contacts.

J. Onuchic, K. Sanbonmatsu, J. D. Prajapati, 2022, Journal of molecular biology.

Sterically-Confined Rearrangements of SARS-CoV-2 Spike Protein Control Cell Invasion

J. Onuchic, P. Whitford, E. Dodero-Rojas, 2021, bioRxiv.

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection

Joseph H. Lubin, Vinícius G. Contessoto, J. Onuchic, 2022, Molecular biology and evolution.

NEET Proteins: A New Link Between Iron Metabolism, Reactive Oxygen Species, and Cancer.

J. Onuchic, P. Jennings, R. Mittler, 2018, Antioxidants & redox signaling.

J. Onuchic, P. Jennings, R. Mittler, 2015, PloS one.

The Fe-S cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer

F. Morcos, J. Onuchic, P. Jennings, 2015, Proceedings of the National Academy of Sciences.

Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes

F. Morcos, J. Onuchic, H. Levine, 2016, bioRxiv.

Uncovering the statistical physics of 3D chromosomal organization using data-driven modeling.

Vinícius G. Contessoto, J. Onuchic, R. R. Cheng, 2022, Current opinion in structural biology.

Structural Reorganization and Relaxation Dynamics of Axially Stressed Chromosomes

Vinícius G. Contessoto, Michele Di Pierro, J. Onuchic, 2022, bioRxiv.

Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble

J. Onuchic, J. Noel, P. Jennings, 2015, PloS one.

Mechanistic basis of propofol-induced disruption of kinesin processivity

J. Onuchic, B. Jana, S. Gilbert, 2021, Proceedings of the National Academy of Sciences.

Connecting thermal and mechanical protein (un)folding landscapes.

J. Onuchic, J. I. Sulkowska, H. Levine, 2014, Biophysical journal.

Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch

J. Onuchic, H. Lammert, Susmita Roy, 2019, Nucleic acids research.

Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch.

J. Onuchic, Susmita Roy, K. Sanbonmatsu, 2017, Biophysical journal.

Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique

J. Onuchic, N. Socci, 1995, chem-ph/9507003.

Decoding the coupled decision-making of the epithelial-mesenchymal transition and metabolic reprogramming in cancer

J. Onuchic, H. Levine, Madeline Galbraith, 2022, bioRxiv.

Electron Transfer: From Model Compounds to Proteins

J. Onuchic, D. Beratan, 1991 .

An associative memory Hamiltonian model for DNA and nucleosomes

Michele Di Pierro, J. Onuchic, Weiqi Lu, 2022, bioRxiv.

Information storage at the molecular level - The design of a molecular shift register memory

John J. Hopfield, José N. Onuchic, David N. Beratan, 1989 .

Pierced Lasso Topology Controls Function in Leptin.

Roy Wollman, Ellinor Haglund, J. Onuchic, 2017, The journal of physical chemistry. B.

Supplementary text: Direct-coupling analysis of residue co-evolution captures native contacts across many protein families

C. Sander, R. Zecchina, F. Morcos, 2011 .

Quantum tunneling in biological reactions: the interplay between theory and experiments

J. Onuchic, K. Baldridge, C. Kobayashi, 2008 .

ELECTRON-TRANSFER TUBES

J. Onuchic, J. Regan, 2007 .

Molecular bridge effects on distant charge tunneling

J. Onuchic, D. Beratan, 1987 .

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.

A Stevedore's Protein Knot

Joanna I. Sulkowska, Hsiao-Ping Hsu, José N. Onuchic, 2010, PLoS Comput. Biol..

Energy landscapes, glass transitions, and chemical reaction dynamics in biomolecular or solvent environment

J. Onuchic, P. Wolynes, 1993 .

KINETICS OF PROTEINLIKE MODELS : THE ENERGY LANDSCAPE FACTORS THAT DETERMINE FOLDING

J. Onuchic, M. Betancourt, 1995 .

Influence of intersite modes on the exchange interaction in electron transfer at large distances

J. Onuchic, A. D. Gama, 1986 .

Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation.

J. Onuchic, Susmita Roy, S. Hennelly, 2021, The journal of physical chemistry. B.

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.

Electron tunneling pathways in ruthenated proteins

José N. Onuchic, David N. Beratan, Harry B. Gray, 1990 .

Multiple versus single pathways in electron transfer in proteins: Influence of protein dynamics and hydrogen bonds

J. Onuchic, K. Baldridge, C. Kobayashi, 2003 .

Different Scenarios for Inter-Protein Electron Tunneling: The Effect of Water-Mediated Pathways

J. Onuchic, O. Miyashita, H. Axelrod, 2002, Journal of biological physics.

Estimating the effect of protein dynamics on electron transfer to the special pair in the photosynthetic reaction center

P. Beroza, J. Onuchic, A. Aquino, 1997 .

Adiabaticity and nonadiabaticity in bimolecular outer‐sphere charge transfer reactions

J. Onuchic, D. Beratan, 1988 .

Some aspects of electron-transfer reaction dynamics

J. Hopfield, J. Onuchic, D. Beratan, 1986 .

Decoding leader cells in collective cancer invasion

J. Onuchic, P. Wong, H. Levine, 2021, Nature Reviews Cancer.

Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools

J. Onuchic, S. Libutti, V. Cristini, 2021, bioRxiv.

Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion

J. Onuchic, M. Di Pierro, Sumitabha Brahmachari, 2022, bioRxiv.

The Unique Cysteine Knot Regulates the Pleotropic Hormone Leptin

José N. Onuchic, Patricia A. Jennings, Ellinor Haglund, 2012, PloS one.

Toward understanding cancer stem cell heterogeneity in the tumor microenvironment

E. Ben-Jacob, J. Onuchic, H. Levine, 2018, Proceedings of the National Academy of Sciences.

Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization.

J. Onuchic, Fernando Bruno da Silva, V. B. Leite, 2021, The journal of physical chemistry. B.

Interrogating the topological robustness of gene regulatory circuits by randomization

Bin Huang, Dongya Jia, Eshel Ben-Jacob, 2017, PLoS Comput. Biol..

Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer

J. Onuchic, H. Levine, M. Jolly, 2020, British Journal of Cancer.

Kinesin's backsteps under mechanical load.

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

Specific and nonspecific collapse in protein folding funnels.

J. Onuchic, N. Socci, H. Nymeyer, 2002, Physical review letters.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Roy G van Heesbeen, Hans H. Cheng, F. Di Palma, 2021, Science.

Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues

J. Onuchic, P. Wolynes, E. Aiden, 2022, bioRxiv.

Targeting CPT1A-mediated fatty acid oxidation sensitizes nasopharyngeal carcinoma to radiation therapy

J. Onuchic, A. Bode, Q. Gao, 2018, Theranostics.

The Energetics and Physiological Impact of Cohesin Extrusion

Neva C. Durand, Erez Lieberman Aiden, Michele Di Pierro, 2018, Cell.

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.

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

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

Epithelial-mesenchymal transition in cancer

J. Onuchic, H. Levine, M. Jolly, 2020, Phenotypic Switching.

Theoretical and computational tools to model multistable gene regulatory networks

J. Onuchic, Q. Nie, Federico Bocci, 2023, ArXiv.

Interactions between mitoNEET and NAF-1 in cells

F. Morcos, J. Onuchic, P. Jennings, 2017, PloS one.

NAF-1 and mitoNEET are central to human breast cancer proliferation by maintaining mitochondrial homeostasis and promoting tumor growth

J. Onuchic, A. Hochberg, P. Jennings, 2013, Proceedings of the National Academy of Sciences.

Nonlinear susceptibilities of finite conjugated organic polymers

José N. Onuchic, Joseph W. Perry, David N. Beratan, 1987 .

Distinguishing mechanisms underlying EMT tristability

E. Ben-Jacob, J. Onuchic, S. Hanash, 2017, bioRxiv.

Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis

Eshel Ben-Jacob, Mingyang Lu, Bin Huang, 2015, Scientific Reports.

Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype

E. Ben-Jacob, J. Onuchic, Shiladitya Sengupta, 2016, Journal of The Royal Society Interface.

Proposed mechanism for stability of proteins to evolutionary mutations.

J. Onuchic, E. Nelson, J N Onuchic, 1998, Proceedings of the National Academy of Sciences of the United States of America.

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

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

Consensus report of the 8 and 9th Weinman Symposia on Gene x Environment Interaction in carcinogenesis: novel opportunities for precision medicine

J. Onuchic, K. Mikoshiba, N. Rothman, 2018, Cell Death & Differentiation.

Forging tools for refining predicted protein structures

Wei Lu, Xun Chen, Mingchen Chen, 2019, Proceedings of the National Academy of Sciences.

1 Supplemental Information

Paul C. Whitford, Karissa Y. Sanbonmatsu, Pawel A. Penczek, 2008 .

Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins

J. Onuchic, A. Kolomeisky, M. Diehl, 2018, Proceedings of the National Academy of Sciences.

Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain

R. Sidman, J. Onuchic, S. Libutti, 2021, Proceedings of the National Academy of Sciences.

Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain

R. Sidman, J. Onuchic, S. Libutti, 2021, bioRxiv.

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.

Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro

J. Onuchic, E. Dodero-Rojas, V. B. Leite, 2020, PloS one.

Modeling Mayaro and Chikungunya Control Strategies in Rio de Janeiro Outbreaks

J. Onuchic, E. Dodero-Rojas, V. B. Leite, 2019, bioRxiv.

Contact map dependence of a T-cell receptor binding repertoire.

Jason T. George, J. Onuchic, Xingcheng Lin, 2021, Physical review. E.

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.

Excited states of ribosome translocation revealed through integrative molecular modeling

Florence Tama, José N. Onuchic, Paul C. Whitford, 2011, Proceedings of the National Academy of Sciences.

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

Jeffrey K. Noel, José N. Onuchic, Paul C. Whitford, 2010, Nucleic Acids Res..

Gambogic acid identifies an isoform-specific druggable pocket in the middle domain of Hsp90β

J. Onuchic, L. Neckers, P. Jennings, 2016, Proceedings of the National Academy of Sciences.

Redox-dependent gating of VDAC by mitoNEET

J. Onuchic, P. Jennings, R. Mittler, 2019, Proceedings of the National Academy of Sciences.

A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity.

J. Onuchic, P. Jennings, J. Adams, 2007, Journal of molecular biology.

Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation.

Osamu Miyashita, Virgil L. Woods, Meghan T. Miller, 2005, Journal of Molecular Biology.

Dynamic coupling between the SH2 domain and active site of the COOH terminal Src kinase, Csk.

Osamu Miyashita, Virgil L. Woods, Jennifer Shaffer, 2004, Journal of molecular biology.

The physics of bacterial decision making

Eshel Ben-Jacob, Daniel Schultz, Mingyang Lu, 2014, Front. Cell. Infect. Microbiol..

Deciding fate in adverse times: Sporulation and competence in Bacillus subtilis

Peter G. Wolynes, José N. Onuchic, Daniel Schultz, 2009, Proceedings of the National Academy of Sciences.

Construction of an effective landscape for multistate genetic switches.

Eshel Ben-Jacob, Mingyang Lu, José Onuchic, 2014, Physical review letters.

Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays

Eshel Ben-Jacob, Mingyang Lu, Yoko Suzuki, 2016, Scientific Reports.

RACIPE: a computational tool for modeling gene regulatory circuits using randomization

Bin Huang, Dongya Jia, José N. Onuchic, 2017, bioRxiv.

An integrated mechanobiochemical feedback mechanism describes chromosome motility from prometaphase to anaphase in mitosis

J. Onuchic, T. Hwa, A. Desai, 2008, Proceedings of the National Academy of Sciences.

A mechanobiochemical mechanism for monooriented chromosome oscillation in mitosis

J. Onuchic, T. Hwa, A. Desai, 2007, Proceedings of the National Academy of Sciences.

Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma.

G. Rangarajan, J. Onuchic, J. Orban, 2022, Biophysics reviews.

A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes.

Antonio B Oliveira Junior, Vinícius G Contessoto, Matheus F Mello, 2020, Journal of molecular biology.

Deciphering the structure of the condensin protein complex

J. Onuchic, R. R. Cheng, M. Di Pierro, 2018, Proceedings of the National Academy of Sciences.

A Transferable Model For Chromosome Architecture

Michele Di Pierro, J. Onuchic, P. Wolynes, 2016, bioRxiv.

Molecular Simulations Suggest a Force-Dependent Mechanism of Vinculin Activation.

J. Onuchic, H. Levine, J. Noel, 2017, Biophysical journal.

Examining the Ensembles of Amyloid-β Monomer Variants and their Propensities to Form Fibers Using an Energy Landscape Visualization Method

Murilo N. Sanches, Antonio B. Oliveira, J. Onuchic, 2021, bioRxiv.

Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms.

J. Onuchic, Prakash Kulkarni, Xingcheng Lin, 2021, Journal of chemical theory and computation.

Massive conformation change in the prion protein: Using dual‐basin structure‐based models to find misfolding pathways

J. Onuchic, P. Whitford, J. Singh, 2012, Proteins.

Evolutionary differences in the ACE2 reveals the molecular origins of COVID-19 susceptibility

J. Onuchic, R. R. Cheng, M. Di Pierro, 2021, bioRxiv.

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

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

The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease

J. Onuchic, P. Jennings, P. Carloni, 2018, JBIC Journal of Biological Inorganic Chemistry.

Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates

J. Onuchic, P. Jennings, R. Mittler, 2017, Scientific Reports.

Breast cancer tumorigenicity is dependent on high expression levels of NAF-1 and the lability of its Fe-S clusters

J. Onuchic, P. Jennings, R. Mittler, 2016, Proceedings of the National Academy of Sciences.

Activation of apoptosis in NAF-1-deficient human epithelial breast cancer cells

J. Onuchic, P. Jennings, S. H. Holt, 2016, Journal of Cell Science.

Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1

F. Morcos, J. Onuchic, P. Jennings, 2014, Proceedings of the National Academy of Sciences.

Allosteric control in a metalloprotein dramatically alters function

Aina E Cohen, Rachel Nechushtai, J. Onuchic, 2012, Proceedings of the National Academy of Sciences.

Interdomain communication revealed in the diabetes drug target mitoNEET

J. Onuchic, P. Jennings, E. L. Baxter, 2011, Proceedings of the National Academy of Sciences.

Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification

J. Onuchic, A. Levchenko, Federico Bocci, 2022, bioRxiv.

Quantum and classical dynamics in biochemical reactions

W. Bialek, J. Joseph, J. Onuchic, 2004, Photosynthesis Research.

Energy landscape along an enzymatic reaction trajectory: Hinges or cracks?

Paul Charles Whitford, J. Onuchic, P. Wolynes, 2008, HFSP journal.

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.

Phylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin

J. Onuchic, P. Jennings, R. Mittler, 2018, Scientific Reports.

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.

Energetic frustration and the nature of the transition state ensemble in protein folding

J. Onuchic, J. Shea, 2000 .

DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases

J. Onuchic, H. Levine, Shubham Tripathi, 2021, bioRxiv.

Extracting function from a β-trefoil folding motif

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

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.

Pierced Lasso Bundles Are a New Class of Knot-like Motifs

Joanna I. Sulkowska, Jeffrey K. Noel, Heiko Lammert, 2014, PLoS Comput. Biol..

Docking and electron transfer between cytochrome c2 and the photosynthetic reaction center

P. Beroza, J. Onuchic, D. Beratan, 1995 .

The two-state reduction for electron and hole transfer in bridge-mediated electron-transfer reactions

J. Onuchic, D. Beratan, S. Skourtis, 1993 .

Electron tunneling pathways in proteins : a method to compute tunneling matrix elements in very large systems

José N. Onuchic, David N. Beratan, J. Onuchic, 1991 .

Interprotein electron transfer from cytochrome c2 to photosynthetic reaction center: tunneling across an aqueous interface.

J. Onuchic, O. Miyashita, M. Okamura, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Dynamics of electron transfer pathways in cytochrome C oxidase.

Ilya A. Balabin, J. Onuchic, I. Balabin, 2004, Biophysical journal.

Dynamically controlled protein tunneling paths in photosynthetic reaction centers.

Ilya A. Balabin, J. Onuchic, I. Balabin, 2000, Science.

Electron transfer in proteins: a novel approach for the description of donor-acceptor coupling

J. Onuchic, J. Regan, S. Skourtis, 1994 .

A new look at the primary charge separation in bacterial photosynthesis

W. Bialek, J. Onuchic, A. Silva, 1992 .

A predictive theoretical model for electron tunneling pathways in proteins

José N. Onuchic, David N. Beratan, J. Onuchic, 1990 .

Exploring the protein folding funnel landscape

J. Onuchic, N. Socci, H. Nymeyer, 1997 .

Direct coupling analysis for protein contact prediction.

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

Lowered pH Leads to Fusion Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin.

J. Onuchic, Jianpeng Ma, J. Noel, 2016, The journal of physical chemistry. B.

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.

Structure and Dynamics of Solvent Landscapes in Charge-Transfer Reactions

J. Onuchic, V. B. Leite, 1996 .

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.

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.

Continuum electrostatic model for the binding of cytochrome c2 to the photosynthetic reaction center from Rhodobacter sphaeroides.

J. Onuchic, O. Miyashita, M. Okamura, 2003, Biochemistry.

Exploring biomolecular machines: energy landscape control of biological reactions

J. Onuchic, O. Miyashita, P. Jennings, 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

Educating future scientists

José N. Onuchic, Elizabeth D. Getzoff, Nancy J. Kopell, 2001, Nature.

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.

Effect of friction on electron transfer: The two reaction coordinate case

J. Onuchic, 1987 .

SMOG 2: A Versatile Software Package for Generating Structure-Based Models

Ryan L. Hayes, Jeffrey K. Noel, Mariana Levi, 2016, PLoS Comput. Biol..

Pathway analysis of protein electron-transfer reactions.

J. Onuchic, H. Gray, D. Beratan, 1992, Annual review of biophysics and biomolecular structure.

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.

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.

Multiple routes lead to the native state in the energy landscape of the β-trefoil family

Leslie L. Chavez, J. Onuchic, P. Jennings, 2006, Proceedings of the National Academy of Sciences.

Knotting a Protein in Explicit Solvent

Joanna I. Sulkowska, Jeffrey K. Noel, José N. Onuchic, 2013 .

A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling

Jason T. George, J. Onuchic, H. Levine, 2018, bioRxiv.

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.

Knotting pathways in proteins.

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

Energy landscape of knotted protein folding

Jeffrey K Noel, Joanna I Sułkowska, J. Onuchic, 2012, Proceedings of the National Academy of Sciences.

A magnesium-induced triplex pre-organizes the SAM-II riboswitch

Bin Chen, Ryan L. Hayes, Heiko Lammert, 2017, PLoS Comput. Biol..

Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification

J. Onuchic, A. Levchenko, Qing Nie, 2023, bioRxiv.

Mapping electron tunneling pathways: an algorithm that finds the "minimum length"/maximum coupling pathway between electron donors and acceptors in proteins

José N. Onuchic, David N. Beratan, Jonathan N. Betts, 1992 .

Tunneling pathway and redox-state-dependent electronic couplings at nearly fixed distance in electron transfer proteins

J. Onuchic, D. Beratan, J. Betts, 1992 .

Tribute to David N. Beratan.

J. Onuchic, M. Therien, I. Rubtsov, 2020, The journal of physical chemistry. B.

Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway

J. Onuchic, Madeline Galbraith, F. Bocci, 2022, PLoS Comput. Biol..

Jagged mediates differences in normal and tumor angiogenesis by affecting tip-stalk fate decision

E. Ben-Jacob, J. Onuchic, M. Jolly, 2015, Proceedings of the National Academy of Sciences.

A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics

F. Morcos, J. Onuchic, P. Jennings, 2022, Proceedings of the National Academy of Sciences.

The anti-apoptotic proteins NAF-1 and iASPP interact to drive apoptosis in cancer cells† †Electronic supplementary information (ESI) available: Experimental section Fig. S1–S4 and Tables S1–S4. See DOI: 10.1039/c8sc03390k

J. Onuchic, P. Jennings, R. Mittler, 2018, Chemical science.

ELECTRON TRANSPORT IN DISORDERED POLYMERIC AND BIOLOGICAL SYSTEMS

V. Pande, J. Onuchic, 1997 .

Expanding Direct Coupling Analysis to Identify Heterodimeric Interfaces from Limited Protein Sequence Data.

J. Onuchic, R. R. Cheng, Kareem M Mehrabiani, 2021, The journal of physical chemistry. B.

Designing bacterial signaling interactions with coevolutionary landscapes

F. Morcos, J. Onuchic, H. Levine, 2018, PloS one.

Guiding the design of bacterial signaling interactions using a coevolutionary landscape

F. Morcos, J. Onuchic, R. R. Cheng, 2017, bioRxiv.

Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control

J. Onuchic, B. Jana, R. N. Manna, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity

José N. Onuchic, Biman Jana, J. Onuchic, 2016, PLoS Comput. Biol..

Nrf2 Modulates the Hybrid Epithelial/Mesenchymal Phenotype and Notch Signaling During Collective Cancer Migration

J. Onuchic, H. Levine, M. Jolly, 2021, bioRxiv.

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.

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.

Temporally correlated active forces drive chromosome structure and dynamics

J. Onuchic, F. MacKintosh, Sumitabha Brahmachari, 2023, bioRxiv.

Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome.

J. Onuchic, P. Whitford, K. Sanbonmatsu, 2010, Journal of the American Chemical Society.

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

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

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.

The energy landscape for solvent dynamics in electron transfer reactions: A minimalist model

J. Onuchic, Y. Tanimura, V. B. Leite, 2002 .

Biomolecular Dynamics — Quantum or Classical? Results for Photosynthetic Electron Transfer

W. Bialek, J. Onuchic, R. Goldstein, 1990 .

Equilibrium unfolding of the poly(glutamic acid)20 helix.

Jennifer C. Lee, J. Onuchic, P. Jennings, 2007, Biopolymers.

BAP1 is a novel regulator of HIF-1α

J. Onuchic, S. Pastorino, M. Negrini, 2023, Proceedings of the National Academy of Sciences of the United States of America.

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Neva C. Durand, Erez Lieberman Aiden, Brendan L. O’Connell, 2023, bioRxiv.

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.

Chromosome Modeling on Downsampled Hi-C Maps Enhances the Compartmentalization Signal.

J. Onuchic, E. Aiden, C. P. Estrada, 2021, The journal of physical chemistry. B.

Contacting the protein folding funnel with NMR.

J. Onuchic, J N Onuchic, 1997, Proceedings of the National Academy of Sciences of the United States of America.

The dual-basin landscape in GFP folding

José N Onuchic, Shachi Gosavi, J. Onuchic, 2008, 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.

Mechanisms of protein assembly: lessons from minimalist models.

J. Onuchic, Y. Levy, 2006, Accounts of chemical research.

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.

Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem

Margaret S. Cheung, José N. Onuchic, J. Onuchic, 2003 .

Computational modeling of phosphotransfer complexes in two-component signaling.

Terence Hwa, Martin Weigt, Alexander Schug, 2010, Methods in enzymology.

SCIENCE EDUCATION: Enhanced: Educating Future Scientists

José N. Onuchic, Elizabeth D. Getzoff, Nancy J. Kopell, 2003 .

Chemical physics of protein folding.

J. Onuchic, P. Wolynes, M. Gruebele, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Effect of gatekeepers on the early folding kinetics of a model β-barrel protein

Charles L. Brooks, José N. Onuchic, J. Onuchic, 2003 .

Fast-folding experiments and the topography of protein folding energy landscapes.

J. Onuchic, P. Wolynes, P. Wolynes, 1996, Chemistry & biology.

Theoretical understanding of the interprotein electron transfer between cytochrome c2 and the photosynthetic reaction center

J. Onuchic, O. Miyashita, M. Okamura, 2003 .

The role of atomic level steric effects and attractive forces in protein folding

Heiko Lammert, J. Onuchic, P. Wolynes, 2012, Proteins.

Electron tunneling in azurin: the coupling across a beta-sheet.

J. Onuchic, H. Gray, L. Skov, 1995, Chemistry & biology.

Fluorescent Proteins Detect Host Structural Rearrangements via Electrostatic Mechanism.

P. Rossky, J. Onuchic, H. Lammert, 2018, Journal of the American Chemical Society.

The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors

Changbong Hyeon, José N. Onuchic, Biman Jana, 2012, PLoS Comput. Biol..

Braiding topology and the energy landscape of chromosome organization proteins

Peter G. Wolynes, José N. Onuchic, Aram Davtyan, 2019, Proceedings of the National Academy of Sciences.

Macromolecular assembly of polycystin-2 intracytosolic C-terminal domain

J. Onuchic, G. Germino, L. Onuchic, 2011, Proceedings of the National Academy of Sciences.

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.

Rotation-Activated and Cooperative Zipping Characterize Class I Viral Fusion Protein Dynamics.

J. Onuchic, Nathanial R. Eddy, 2018, Biophysical journal.

PyMEGABASE: Predicting cell-type-specific structural annotations of chromosomes using the epigenome.

Matheus F Mello, J. Onuchic, Sumitabha Brahmachari, 2023, Journal of molecular biology.

Exploring chromosomal structural heterogeneity across multiple cell lines

Erez Lieberman Aiden, J. Onuchic, P. Wolynes, 2020, bioRxiv.

The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome

Peter G. Wolynes, José N. Onuchic, Vinícius G. Contessoto, 2019, bioRxiv.

INAUGURAL ARTICLE by a Recently Elected Academy Member:Deciding fate in adverse times: Sporulation and competence in Bacillus subtilis

J. Onuchic, P. Wolynes, E. Jacob, 2009 .

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.

Physics transforming the life sciences

J. Onuchic, 2014, Physical biology.

Title : A Transferable Model For Chromosome Architecture

Michele Di Pierro, J. Onuchic, P. Wolynes, 2016 .

Structural and energetic heterogeneity in protein folding. I. Theory

José N. Onuchic, Steven S. Plotkin, J. Onuchic, 2002 .

Structural and Energetic Heterogeneity in Protein Folding

Steven S. Plotkin, J. Onuchic, S. Plotkin, 2000, cond-mat/0009412.

Protein dynamics and reaction rates: mode-specific chemistry in large molecules?

W Bialek, W. Bialek, J. Onuchic, 1988, Proceedings of the National Academy of Sciences of the United States of America.

Theoretical and computational tools to model multistable gene regulatory networks

J. Onuchic, M. Jolly, D. Jia, 2023, Reports on progress in physics. Physical Society.

Theoretical and computational tools to model multistable gene regulatory networks

J. Onuchic, Q. Nie, M. Jolly, 2023, ArXiv.

Modeling the response of a tumor-suppressive network to mitogenic and oncogenic signals

J. Onuchic, Xiao-Peng Zhang, Wei Wang, 2017, Proceedings of the National Academy of Sciences.

Electron tunneling pathways in proteins.

J. Onuchic, D. Beratan, J. Winkler, 1992, Current opinion in chemical biology.

The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease

J. Onuchic, P. Jennings, P. Carloni, 2018, JBIC Journal of Biological Inorganic Chemistry.

INAUGURAL ARTICLE by a Recently Elected Academy Member:Deciding fate in adverse times: Sporulation and competence in Bacillus subtilis

J. Onuchic, P. Wolynes, E. Jacob, 2009 .

Symmetry and Kinetic Optimization of Proteinlike Heteropolymers

J. Onuchic, E. Nelson, L. F. Teneyck, 1997 .

Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms

Antonio B. Oliveira, J. Onuchic, Prakash Kulkarni, 2021, bioRxiv.

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.

The Many Faces of Structure-Based Potentials: From Protein Folding Landscapes to Structural Characterization of Complex Biomolecules

J. Onuchic, J. Noel, 2012 .

Molecular origin of the weak susceptibility of kinesin velocity to loads and its relation to the collective behavior of kinesins

Margaret S. Cheung, Anatoly B. Kolomeisky, Michael R. Diehl, 2017, Proceedings of the National Academy of Sciences.

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.

J. Onuchic, P. Jennings, R. Mittler, 2018, Chemical science.

Consensus report of the 8 and 9th Weinman Symposia on Gene x Environment Interaction in carcinogenesis: novel opportunities for precision medicine

J. Onuchic, K. Mikoshiba, N. Rothman, 2018, Cell Death and Differentiation.

Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein

J. Onuchic, P. Jennings, R. Mittler, 2011, Proceedings of the National Academy of Sciences.

Toward decoding the principles of cancer metastasis circuits.

E. Ben-Jacob, J. Onuchic, M. Jolly, 2014, Cancer research.

Excited states of ribosome translocation revealed through integrative molecular modeling

J. Onuchic, F. Tama, C. Spahn, 2011, Proceedings of the National Academy of Sciences.

Theory of protein folding.

J. Onuchic, P. Wolynes, 2004, Current opinion in structural biology.

Physical Chemistry Chemical Physics Physical Chemistry of Biomolecular Motors and Machines Guest Editor: Anatoly Kolomeisky (rice University) Papers Twist–stretch Coupling and Phase Transition during Dna Supercoiling Opening the Arg-glu Salt Bridge in Myosin: Computational Study the Energetics of Al

Adrian W. R. Serohijos, Del R. Jackson, Mark E. Arsenault, 2009 .

Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis

E. Ben-Jacob, J. Onuchic, H. Levine, 2015, Front. Oncol..

Deciphering the Dynamics of Epithelial-Mesenchymal Transition and Cancer Stem Cells in Tumor Progression

J. Onuchic, H. Levine, M. Jolly, 2019, Current Stem Cell Reports.

Nrf2 regulates collective cancer migration by modulating the hybrid epithelial/mesenchymal phenotype

Mohit, J. Onuchic, H. Levine, 2021 .

Adrian W. R. Serohijos, Del R. Jackson, Mark E. Arsenault, 2022 .

Phylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin

J. Onuchic, P. Jennings, R. Mittler, 2018, Scientific Reports.

Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification

J. Onuchic, A. Levchenko, Qing Nie, 2023, bioRxiv.

RNA as a Complex Polymer with Coupled Dynamics of Ions and Water in the Outer Solvation Sphere.

J. Onuchic, H. Lammert, U. Mohanty, 2018, The journal of physical chemistry. B.

Determination of the water geometry in violuric acid monohydrate with a Monte Carlo simulation

J. Onuchic, G. Corongiu, 1988 .

Energy landscape along an enzymatic reaction trajectory: Hinges or cracks?

J. Onuchic, P. Wolynes, P. Whitford, 2008, HFSP journal.

The energy landscape for protein folding and possible connections to function

Leslie L. Chavez, J. Onuchic, Margaret S. Cheung, 2004 .

Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L.

J. Onuchic, A. Garcia, C. Clementi, 2003, Journal of molecular biology.

RACER-m Leverages Structural Features for Sparse T Cell Specificity Prediction

Jason T. George, J. Onuchic, H. Levine, 2023, bioRxiv.

Connecting thermal and mechanical protein (un)folding landscapes.

J. Onuchic, J. I. Sulkowska, H. Levine, 2014, Biophysical journal.

Order and disorder control the functional rearrangement of influenza hemagglutinin

J. Onuchic, Jianpeng Ma, J. Noel, 2014, Proceedings of the National Academy of Sciences.

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

Samuel S. Cho, J. Onuchic, P. Wolynes, 2005, Proceedings of the National Academy of Sciences of the United States of America.

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

J. Onuchic, P. Whitford, S. Blanchard, 2010 .

Conformational Transitions in Adenylate Kinase ALLOSTERIC COMMUNICATION REDUCES MISLIGATION *

J. Onuchic, P. Whitford, S. Gosavi, 2008 .

Proteins at Work

Michael A. Jamros, J. Onuchic, D. Blumenthal, 2010, The Journal of Biological Chemistry.

An analytical study of the interplay between geometrical and energetic effects in protein folding.

J. Onuchic, J. Noel, Yoko Suzuki, 2008, The Journal of chemical physics.

Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion

J. Onuchic, P. Whitford, E. Dodero-Rojas, 2021, eLife.

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.

Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch.

J. Onuchic, Susmita Roy, K. Sanbonmatsu, 2017, Biophysical journal.

Energy landscape of knotted protein folding

J. Onuchic, J. Noel, J. Sulkowska, 2012, Proceedings of the National Academy of Sciences.

Structure of infectious prions: stabilization by domain swapping

J. Onuchic, H. Levine, D. Cox, 2005, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance.

F. Morcos, J. Onuchic, R. Nechushtai, 2024, Proceedings of the National Academy of Sciences of the United States of America.

Modeling the interplay between geometrical and energetic effects in protein folding.

J. Onuchic, Yoko Suzuki, 2005, The journal of physical chemistry. B.