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List of works by José Onuchic

A Stevedore's protein knot

scientific article

A driving and coupling "Pac-Man" mechanism for chromosome poleward translocation in anaphase A.

scholarly article

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

scientific article

A mechanobiochemical mechanism for monooriented chromosome oscillation in mitosis

scholarly article

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

scientific article published on June 28, 2011

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

scientific article published on 26 October 2009

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

scientific article

A structural perspective on the dynamics of kinesin motors

scientific article published in December 2011

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

scientific article

Absolute rate theories of epigenetic stability

scholarly article

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

scientific article

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

scientific article published on 30 November 2015

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

scientific article

Altered backbone and side-chain interactions result in route heterogeneity during the folding of interleukin-1β (IL-1β)

scientific article published on August 2013

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields

scientific article

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

scientific article published in January 2008

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

scholarly article

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

article published in the Proceedings of the National Academy of Sciences of the United States of America

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

scientific article published on 30 September 2008

Biomolecular dynamics: order–disorder transitions and energy landscapes ⬇️

scientific article published on June 28, 2012

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

scientific article published on 12 September 2016

Cancer-Related NEET Proteins Transfer 2Fe-2S Clusters to Anamorsin, a Protein Required for Cytosolic Iron-Sulfur Cluster Biogenesis

scientific article published on 8 October 2015

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

scientific article

Coevolutionary signals across protein lineages help capture multiple protein conformations.

scientific article

Conformational transitions in adenylate kinase. Allosteric communication reduces misligation

scientific article published on 11 November 2007

Conformational transitions of adenylate kinase: switching by cracking

scientific article

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

scientific article

Connecting thermal and mechanical protein (un)folding landscapes

scientific article

Constructing sequence-dependent protein models using coevolutionary information

scientific article published on 30 July 2015

Construction of an effective landscape for multistate genetic switches.

scientific article published on 13 August 2014

Continuum Electrostatic Model for the Binding of Cytochromec2to the Photosynthetic Reaction Center fromRhodobacter sphaeroides ⬇️

scientific article published on October 14, 2003

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

scientific article published in July 2017

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

scientific article published on 31 October 2017

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

scientific article

Designing bacterial signaling interactions with coevolutionary landscapes

scientific article published in PLoS ONE

Dimeric interactions and complex formation using direct coevolutionary couplings

scientific article

Direct coupling analysis for protein contact prediction.

scientific article

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

scientific article published on 08 June 2009

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

scientific article

Distinguishing mechanisms underlying EMT tristability

article published in 2017

Dodging the crisis of folding proteins with knots

scientific article

Domain swapping is a consequence of minimal frustration

scholarly article

Effective stochastic dynamics on a protein folding energy landscape

scientific article

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

scientific article

Excited states of ribosome translocation revealed through integrative molecular modeling ⬇️

scientific article published on November 11, 2011

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

scientific article published on 19 April 2021

Exploring biomolecular machines: energy landscape control of biological reactions

scientific article

Exploring chromosomal structural heterogeneity across multiple cell lines

scientific article published on 13 October 2020

Extinction and resurrection in gene networks

scholarly article

Extracting function from a beta-trefoil folding motif

scientific article

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

scientific article

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

scientific article published in January 2007

Folding Circular Permutants of IL-1β: Route Selection Driven by Functional Frustration ⬇️

scientific article (publication date: 2012)

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

scientific article published on November 17, 2003

Folding a protein in the computer: reality or hope?

scientific article

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

scientific article published on 25 February 2013

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

scientific article published on October 14, 2010

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

scientific article published in July 2004

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere.

scientific article

Genomics-aided structure prediction

scientific article

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

scientific article published on 2 December 2015

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

scientific article

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

scientific article

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

scientific article

Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins

scientific article published on 18 December 2012

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

scientific article published on 27 January 2016

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

scientific article published on 25 March 2014

Intercellular stress reconstitution from traction force data

scientific article

Interdomain communication revealed in the diabetes drug target mitoNEET ⬇️

scientific article published on March 14, 2011

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

scholarly article

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

scientific article

Kinesin's backsteps under mechanical load

scientific article published on 18 May 2009

Learning from cancer how to defeat bacteria

scientific article published on 13 February 2013

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

scientific article

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

scientific article published on 19 August 2016

Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch ⬇️

scientific article published on July 16, 2012

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

scientific article published on 13 February 2012

Mechanical control of the directional stepping dynamics of the kinesin motor

scholarly article

Mechanisms of protein assembly: lessons from minimalist models

scientific article

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

scientific article

Mirror images as naturally competing conformations in protein folding.

scientific article

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

scientific article

Modeling the interplay between geometrical and energetic effects in protein folding

scientific article

Molecular Simulations Suggest a Force-Dependent Mechanism of Vinculin Activation

scientific article

Molecular level stochastic model for competence cycles in Bacillus subtilis

scholarly article

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

article published in the Proceedings of the National Academy of Sciences of the United States of America

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

scientific article

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

scholarly article

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

scholarly article

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

scientific article published on 19 August 2013

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

scientific article published on January 2009

Order and disorder control the functional rearrangement of influenza hemagglutinin

scientific article

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

scientific article

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

scientific article published on 15 February 2016

Physics transforming the life sciences

scientific article published on 8 October 2014

Pierced Lasso Bundles are a new class of knot-like motifs

scientific article

Preface to Special Topic on Protein Dynamics: Beyond Static Snapshots in Structural Biology

scientific article published on January 2016

Probing the kinetics of single molecule protein folding

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published in September 2005

Protein topology determines binding mechanism

scientific article published on 23 December 2003

Proteins at work: a combined small angle X-RAY scattering and theoretical determination of the multiple structures involved on the protein kinase functional landscape

scientific article

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

scientific article published in July 2004

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

scientific article

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

scientific article published on 27 August 2018

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

scientific article published on April 2014

Robustness and generalization of structure-based models for protein folding and function.

scientific article published in December 2009

Role of metabolic spatiotemporal dynamics in regulating biofilm colony expansion.

scientific article published on 2 April 2018

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Special issue on protein folding: experimental and theoretical approaches.

scientific article

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

scientific article published on 31 August 2021

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

scientific article published on 21 July 2022

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

scientific article

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

scientific article published on January 23, 2012

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

article published in the Proceedings of the National Academy of Sciences of the United States of America

Structure of infectious prions: stabilization by domain swapping

scientific article published in November 2005

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

scientific article published on 19 December 2017

Structure-Based Model of RNA Pseudoknot Captures Magnesium-Dependent Folding Thermodynamics

scientific article published on 07 February 2019

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

scientific article published on September 20, 2012

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

scientific article

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

scientific article

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

scientific article published on 08 October 2018

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

scientific article

The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function ⬇️

scientific article published on May 11, 2012

The Unique Cysteine Knot Regulates the Pleotropic Hormone Leptin ⬇️

scientific article published on September 24, 2012

The dominant folding route minimizes backbone distortion in SH3.

scientific article published on 15 November 2012

The dual-basin landscape in GFP folding

scholarly article

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

scientific article

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

scientific article published in April 2005

The origin of minus-end directionality and mechanochemistry of Ncd motors

scientific article (publication date: 2012)

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

scientific article

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

scientific article published on November 12, 2011

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

scientific article

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

scientific article published in November 1996

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

scientific article

Topological frustration and the folding of interleukin-1 beta

scientific article published on 9 December 2005

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

scientific article published on 21 January 2014

Transferable model for chromosome architecture

scientific article published on 29 September 2016

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

scholarly article

Tribute to David N. Beratan

scientific article published on 01 April 2020

Tribute to Peter G. Wolynes

scientific article published in October 2013

Tristability in cancer-associated microRNA-TF chimera toggle switch

scientific article published on 30 May 2013

Turning death into creative force during biofilm engineering ⬇️

scientific article published on November 13, 2012

Turning oscillations into opportunities: lessons from a bacterial decision gate

scientific article

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

scientific article

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

scientific article

Understanding stochastic simulations of the smallest genetic networks

scientific article published in June 2007

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

scientific article published on 26 December 2018

Water and proteins: a love-hate relationship

scholarly article

Water mediation in protein folding and molecular recognition

scientific article

What protein folding teaches us about biological function and molecular machines

scientific article published on 02 January 2015

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

scientific article published on January 17, 2012

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