José Nelson Onuchic - Publications

Affiliations: 
1990-2011 Physics University of California, San Diego, La Jolla, CA 
 2011- Physics Rice University, Houston, TX 
Area:
Theoretical Biological Physics
Website:
https://chemistry.rice.edu/FacultyDetail.aspx?p=51BE2F2C673C5991

261 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Lipper CH, Stofleth JT, Bai F, Sohn YS, Roy S, Mittler R, Nechushtai R, Onuchic JN, Jennings PA. Redox-dependent gating of VDAC by mitoNEET. Proceedings of the National Academy of Sciences of the United States of America. PMID 31527235 DOI: 10.1073/pnas.1908271116  0.8
2019 Bocci F, Tripathi SC, Vilchez Mercedes SA, George JT, Casabar JP, Wong PK, Hanash SM, Levine H, Onuchic JN, Jolly MK. NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype. Integrative Biology : Quantitative Biosciences From Nano to Macro. PMID 31329868 DOI: 10.1093/intbio/zyz021  0.96
2019 Jia D, Li X, Bocci F, Tripathi S, Deng Y, Jolly MK, Onuchic JN, Levine H. Quantifying Cancer Epithelial-Mesenchymal Plasticity and its Association with Stemness and Immune Response. Journal of Clinical Medicine. 8. PMID 31121840 DOI: 10.3390/jcm8050725  0.96
2019 Morcos F, Onuchic JN. The role of coevolutionary signatures in protein interaction dynamics, complex inference, molecular recognition, and mutational landscapes. Current Opinion in Structural Biology. 56: 179-186. PMID 31029927 DOI: 10.1016/j.sbi.2019.03.024  0.64
2019 Lin X, Schafer NP, Lu W, Jin S, Chen X, Chen M, Onuchic JN, Wolynes PG. Forging tools for refining predicted protein structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 31000596 DOI: 10.1073/pnas.1900778116  0.92
2019 Lin X, Kulkarni P, Bocci F, Schafer NP, Roy S, Tsai MY, He Y, Chen Y, Rajagopalan K, Mooney SM, Zeng Y, Weninger K, Grishaev A, Onuchic JN, Levine H, et al. Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level. Biomolecules. 9. PMID 30813315 DOI: 10.3390/biom9020077  0.96
2019 Iosub-Amir A, Bai F, Sohn YS, Song L, Tamir S, Marjault HB, Mayer G, Karmi O, Jennings PA, Mittler R, Onuchic JN, Friedler A, Nechushtai R. The anti-apoptotic proteins NAF-1 and iASPP interact to drive apoptosis in cancer cells. Chemical Science. 10: 665-673. PMID 30774867 DOI: 10.1039/c8sc03390k  0.8
2019 Jia D, Lu M, Jung KH, Park JH, Yu L, Onuchic JN, Kaipparettu BA, Levine H. Elucidating cancer metabolic plasticity by coupling gene regulation with metabolic pathways. Proceedings of the National Academy of Sciences of the United States of America. PMID 30733294 DOI: 10.1073/pnas.1816391116  0.96
2019 Mandic A, Hayes RL, Lammert H, Cheng RR, Onuchic JN. Structure-Based Model of RNA Pseudoknot Captures Magnesium-dependent Folding Thermodynamics. The Journal of Physical Chemistry. B. PMID 30676755 DOI: 10.1021/acs.jpcb.8b10791  0.64
2019 Roy S, Hennelly SP, Lammert H, Onuchic JN, Sanbonmatsu KY. Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch. Nucleic Acids Research. PMID 30605518 DOI: 10.1093/nar/gky1311  0.92
2018 Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SH, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, ... ... Onuchic JN, et al. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. Plos Genetics. 14: e1007872. PMID 30586358 DOI: 10.1371/journal.pgen.1007872  0.6
2018 Jia D, George J, Tripathi S, Kundnani D, Lu M, Hanash S, Onuchic J, Jolly MK, Levine H. Testing the gene expression classification of the EMT spectrum. Physical Biology. PMID 30557866 DOI: 10.1088/1478-3975/aaf8d4  0.96
2018 Krepel D, Cheng RR, Di Pierro M, Onuchic JN. Deciphering the structure of the condensin protein complex. Proceedings of the National Academy of Sciences of the United States of America. PMID 30385633 DOI: 10.1073/pnas.1812770115  0.6
2018 Dutta M, Diehl MR, Onuchic JN, Jana B. Structural consequences of hereditary spastic paraplegia disease-related mutations in kinesin. Proceedings of the National Academy of Sciences of the United States of America. PMID 30366951 DOI: 10.1073/pnas.1810622115  0.56
2018 Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, ... ... Onuchic JN, et al. The Energetics and Physiological Impact of Cohesin Extrusion. Cell. 175: 292-294. PMID 30241609 DOI: 10.1016/j.cell.2018.09.002  0.64
2018 Chen M, Lin X, Lu W, Schafer NP, Onuchic JN, Wolynes PG. Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields. Journal of Chemical Theory and Computation. PMID 30240202 DOI: 10.1021/acs.jctc.8b00683  0.92
2018 Wang Q, Jana B, Diehl MR, Cheung MS, Kolomeisky AB, Onuchic JN. Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins. Proceedings of the National Academy of Sciences of the United States of America. PMID 30224489 DOI: 10.1073/pnas.1806688115  0.88
2018 Cheng RR, Haglund E, Tiee NS, Morcos F, Levine H, Adams JA, Jennings PA, Onuchic JN. Designing bacterial signaling interactions with coevolutionary landscapes. Plos One. 13: e0201734. PMID 30125296 DOI: 10.1371/journal.pone.0201734  0.96
2018 Lammert H, Wang A, Mohanty U, Onuchic JN. RNA as a Complex Polymer with Coupled Dynamics of Ions and Water in the Outer Solvation Sphere. The Journal of Physical Chemistry. B. PMID 30102033 DOI: 10.1021/acs.jpcb.8b06874  0.64
2018 Lin X, Noel JK, Wang Q, Ma J, Onuchic JN. Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill. Proceedings of the National Academy of Sciences of the United States of America. PMID 30012616 DOI: 10.1073/pnas.1805442115  0.92
2018 Di Pierro M, Potoyan DA, Wolynes PG, Onuchic JN. Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes. Proceedings of the National Academy of Sciences of the United States of America. PMID 29987017 DOI: 10.1073/pnas.1806297115  0.92
2018 Huang B, Jia D, Feng J, Levine H, Onuchic JN, Lu M. RACIPE: a computational tool for modeling gene regulatory circuits using randomization. Bmc Systems Biology. 12: 74. PMID 29914482 DOI: 10.1186/s12918-018-0594-6  0.96
2018 Lin X, Roy S, Jolly MK, Bocci F, Schafer NP, Tsai MY, Chen Y, He Y, Grishaev A, Weninger K, Orban J, Kulkarni P, Rangarajan G, Levine H, Onuchic JN. PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer. Journal of Molecular Biology. PMID 29758263 DOI: 10.1016/j.jmb.2018.05.011  0.96
2018 Tan Z, Xiao L, Tang M, Bai F, Li J, Li L, Shi F, Li N, Li Y, Du Q, Lu J, Weng X, Yi W, Zhang H, Fan J, ... ... Onuchic JN, et al. Targeting CPT1A-mediated fatty acid oxidation sensitizes nasopharyngeal carcinoma to radiation therapy. Theranostics. 8: 2329-2347. PMID 29721083 DOI: 10.7150/thno.21451  0.8
2018 Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, ... ... Onuchic JN, et al. The Energetics and Physiological Impact of Cohesin Extrusion. Cell. PMID 29706548 DOI: 10.1016/j.cell.2018.03.072  0.64
2018 Eddy NR, Onuchic JN. Rotation-Activated and Cooperative Zipping Characterize Class I Viral Fusion Protein Dynamics. Biophysical Journal. 114: 1878-1888. PMID 29694865 DOI: 10.1016/j.bpj.2018.03.005  0.6
2018 Bocci F, Suzuki Y, Lu M, Onuchic JN. Role of metabolic spatiotemporal dynamics in regulating biofilm colony expansion. Proceedings of the National Academy of Sciences of the United States of America. PMID 29610314 DOI: 10.1073/pnas.1706920115  0.64
2018 Mittler R, Darash-Yahana M, Sohn YS, Bai F, Song L, Cabantchik IZ, Jennings P, Onuchic J, Nechushtai R. NEET proteins: A new link between iron metabolism, ROS and cancer. Antioxidants & Redox Signaling. PMID 29463105 DOI: 10.1089/ars.2018.7502  0.8
2018 Simine L, Lammert H, Sun L, Onuchic JN, Rossky PJ. Fluorescent proteins detect host structural rearrangements via electrostatic mechanism. Journal of the American Chemical Society. PMID 29328673 DOI: 10.1021/jacs.7b10851  0.88
2017 Jia D, Jolly MK, Tripathi SC, Den Hollander P, Huang B, Lu M, Celiktas M, Ramirez-Peña E, Ben-Jacob E, Onuchic JN, Hanash SM, Mani SA, Levine H. Distinguishing mechanisms underlying EMT tristability. Cancer Convergence. 1: 2. PMID 29623961 DOI: 10.1186/s41236-017-0005-8  0.96
2017 Lipper CH, Karmi O, Sohn YS, Darash-Yahana M, Lammert H, Song L, Liu A, Mittler R, Nechushtai R, Onuchic JN, Jennings PA. Structure of the human monomeric NEET protein MiNT and its role in regulating iron and reactive oxygen species in cancer cells. Proceedings of the National Academy of Sciences of the United States of America. PMID 29259115 DOI: 10.1073/pnas.1715842115  0.64
2017 Bocci F, Jolly MK, Tripathi SC, Aguilar M, Hanash SM, Levine H, Onuchic JN. Numb prevents a complete epithelial-mesenchymal transition by modulating Notch signalling. Journal of the Royal Society, Interface. 14. PMID 29187638 DOI: 10.1098/rsif.2017.0512  0.96
2017 Di Pierro M, Cheng RR, Lieberman Aiden E, Wolynes PG, Onuchic JN. De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture. Proceedings of the National Academy of Sciences of the United States of America. PMID 29087948 DOI: 10.1073/pnas.1714980114  0.92
2017 Sun L, Noel JK, Levine H, Onuchic JN. Molecular Simulations Suggest a Force-Dependent Mechanism of Vinculin Activation. Biophysical Journal. 113: 1697-1710. PMID 29045864 DOI: 10.1016/j.bpj.2017.08.037  0.96
2017 Wang Q, Diehl MR, Jana B, Cheung MS, Kolomeisky AB, Onuchic JN. Molecular origin of the weak susceptibility of kinesin velocity to loads and its relation to the collective behavior of kinesins. Proceedings of the National Academy of Sciences of the United States of America. PMID 28973894 DOI: 10.1073/pnas.1710328114  0.88
2017 Roy S, Onuchic JN, Sanbonmatsu KY. Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch. Biophysical Journal. 113: 348-359. PMID 28746845 DOI: 10.1016/j.bpj.2017.06.044  0.92
2017 Tian X, Huang B, Zhang XP, Lu M, Liu F, Onuchic JN, Wang W. Modeling the response of a tumor-suppressive network to mitogenic and oncogenic signals. Proceedings of the National Academy of Sciences of the United States of America. PMID 28484034 DOI: 10.1073/pnas.1702412114  0.6
2017 Huang B, Lu M, Jia D, Ben-Jacob E, Levine H, Onuchic JN. Interrogating the topological robustness of gene regulatory circuits by randomization. Plos Computational Biology. 13: e1005456. PMID 28362798 DOI: 10.1371/journal.pcbi.1005456  0.96
2017 Roy S, Lammert H, Hayes RL, Chen B, LeBlanc R, Dayie TK, Onuchic JN, Sanbonmatsu KY. A magnesium-induced triplex pre-organizes the SAM-II riboswitch. Plos Computational Biology. 13: e1005406. PMID 28248966 DOI: 10.1371/journal.pcbi.1005406  0.92
2017 Yu L, Lu M, Jia D, Ma J, Ben-Jacob E, Levine H, Kaipparettu BA, Onuchic JN. Modeling the Genetic Regulation of Cancer Metabolism: Interplay Between Glycolysis and Oxidative Phosphorylation. Cancer Research. PMID 28202516 DOI: 10.1158/0008-5472.CAN-16-2074  0.96
2016 Bai F, Morcos F, Cheng RR, Jiang H, Onuchic JN. Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis. Proceedings of the National Academy of Sciences of the United States of America. PMID 27911825 DOI: 10.1073/pnas.1615932113  0.8
2016 Chen M, Lin X, Lu W, Onuchic JN, Wolynes PG. Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins. The Journal of Physical Chemistry. B. PMID 27797194 DOI: 10.1021/acs.jpcb.6b09347  0.92
2016 Di Pierro M, Zhang B, Aiden EL, Wolynes PG, Onuchic JN. Transferable model for chromosome architecture. Proceedings of the National Academy of Sciences of the United States of America. PMID 27688758 DOI: 10.1073/pnas.1613607113  0.92
2016 Darash-Yahana M, Pozniak Y, Lu M, Sohn YS, Karmi O, Tamir S, Bai F, Song L, Jennings PA, Pikarsky E, Geiger T, Onuchic JN, Mittler R, Nechushtai R. Breast cancer tumorigenicity is dependent on high expression levels of NAF-1 and the lability of its Fe-S clusters. Proceedings of the National Academy of Sciences of the United States of America. PMID 27621439 DOI: 10.1073/pnas.1612736113  1
2016 Lin X, Noel JK, Wang Q, Ma J, Onuchic JN. Lowered pH Leads to Fusion Peptide Release and a Highly-Dynamic Intermediate of Influenza Hemagglutinin. The Journal of Physical Chemistry. B. PMID 27541202 DOI: 10.1021/acs.jpcb.6b06775  1
2016 Jana B, Onuchic JN. Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity. Plos Computational Biology. 12: e1005035. PMID 27494025 DOI: 10.1371/journal.pcbi.1005035  0.56
2016 Yim KH, Prince TL, Qu S, Bai F, Jennings PA, Onuchic JN, Theodorakis EA, Neckers L. Gambogic acid identifies an isoform-specific druggable pocket in the middle domain of Hsp90β. Proceedings of the National Academy of Sciences of the United States of America. PMID 27466407 DOI: 10.1073/pnas.1606655113  1
2016 Chen M, Lin X, Zheng W, Onuchic JN, Wolynes PG. Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model (AAWSEM). The Journal of Physical Chemistry. B. PMID 27148634 DOI: 10.1021/acs.jpcb.6b02451  0.92
2016 Noel JK, Levi M, Raghunathan M, Lammert H, Hayes RL, Onuchic JN, Whitford PC. SMOG 2: A Versatile Software Package for Generating Structure-Based Models. Plos Computational Biology. 12: e1004794. PMID 26963394 DOI: 10.1371/journal.pcbi.1004794  1
2016 Noel JK, Morcos F, Onuchic JN. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics. F1000research. 5. PMID 26918164 DOI: 10.12688/f1000research.7186.1  1
2016 Suzuki Y, Lu M, Ben-Jacob E, Onuchic JN. Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays. Scientific Reports. 6: 21037. PMID 26876008 DOI: 10.1038/srep21037  1
2016 Ferreira DC, van der Linden MG, de Oliveira LC, Onuchic JN, Pereira de Araújo AF. Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes. Proteins. PMID 26815167 DOI: 10.1002/prot.24998  1
2015 Lammert H, Noel JK, Haglund E, Schug A, Onuchic JN. Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures. The Journal of Chemical Physics. 143: 243141. PMID 26723626 DOI: 10.1063/1.4936881  1
2015 Fisher KM, Haglund E, Noel JK, Hailey KL, Onuchic JN, Jennings PA. Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble. Plos One. 10: e0144067. PMID 26630011 DOI: 10.1371/journal.pone.0144067  1
2015 Huang B, Jolly MK, Lu M, Tsarfaty I, Ben-Jacob E, Onuchic JN. Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis. Scientific Reports. 5: 17379. PMID 26627083 DOI: 10.1038/srep17379  1
2015 Holt SH, Darash-Yahana M, Sohn YS, Song L, Karmi O, Tamir S, Michaeli D, Luo Y, Paddock ML, Jennings PA, Onuchic JN, Azad RK, Pikarsky E, Cabantchik IZ, Nechushtai R, et al. Activation of apoptosis in NAF-1-deficient human epithelial breast cancer cells. Journal of Cell Science. PMID 26621032 DOI: 10.1242/jcs.178293  1
2015 Lipper CH, Paddock ML, Onuchic JN, Mittler R, Nechushtai R, Jennings PA. Cancer-Related NEET Proteins Transfer 2Fe-2S Clusters to Anamorsin, a Protein Required for Cytosolic Iron-Sulfur Cluster Biogenesis. Plos One. 10: e0139699. PMID 26448442 DOI: 10.1371/journal.pone.0139699  1
2015 dos Santos RN, Morcos F, Jana B, Andricopulo AD, Onuchic JN. Dimeric interactions and complex formation using direct coevolutionary couplings. Scientific Reports. 5: 13652. PMID 26338201 DOI: 10.1038/srep13652  1
2015 Jolly MK, Boareto M, Huang B, Jia D, Lu M, Ben-Jacob E, Onuchic JN, Levine H. Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis. Frontiers in Oncology. 5: 155. PMID 26258068 DOI: 10.3389/fonc.2015.00155  0.96
2015 Cheng RR, Raghunathan M, Noel JK, Onuchic JN. Constructing sequence-dependent protein models using coevolutionary information. Protein Science : a Publication of the Protein Society. PMID 26223372 DOI: 10.1002/pro.2758  1
2015 Hayes RL, Noel JK, Mandic A, Whitford PC, Sanbonmatsu KY, Mohanty U, Onuchic JN. Generalized Manning Condensation Model Captures the RNA Ion Atmosphere. Physical Review Letters. 114: 258105. PMID 26197147 DOI: 10.1103/PhysRevLett.114.258105  1
2015 Boareto M, Jolly MK, Ben-Jacob E, Onuchic JN. Jagged mediates differences in normal and tumor angiogenesis by affecting tip-stalk fate decision. Proceedings of the National Academy of Sciences of the United States of America. 112: E3836-44. PMID 26153421 DOI: 10.1073/pnas.1511814112  1
2015 Bai F, Morcos F, Sohn YS, Darash-Yahana M, Rezende CO, Lipper CH, Paddock ML, Song L, Luo Y, Holt SH, Tamir S, Theodorakis EA, Jennings PA, Onuchic JN, Mittler R, et al. The Fe-S cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 112: 3698-703. PMID 25762074 DOI: 10.1073/pnas.1502960112  1
2015 Kirmizialtin S, Hennelly SP, Schug A, Onuchic JN, Sanbonmatsu KY. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods in Enzymology. 553: 215-34. PMID 25726467 DOI: 10.1016/bs.mie.2014.10.061  1
2015 Boareto M, Jolly MK, Lu M, Onuchic JN, Clementi C, Ben-Jacob E. Jagged-Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype. Proceedings of the National Academy of Sciences of the United States of America. 112: E402-9. PMID 25605936 DOI: 10.1073/pnas.1416287112  1
2015 Whitford PC, Onuchic JN. What protein folding teaches us about biological function and molecular machines. Current Opinion in Structural Biology. 30: 57-62. PMID 25559307 DOI: 10.1016/j.sbi.2014.12.003  1
2015 Tamir S, Paddock ML, Darash-Yahana-Baram M, Holt SH, Sohn YS, Agranat L, Michaeli D, Stofleth JT, Lipper CH, Morcos F, Cabantchik IZ, Onuchic JN, Jennings PA, Mittler R, Nechushtai R. Structure-function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease. Biochimica Et Biophysica Acta. 1853: 1294-1315. PMID 25448035 DOI: 10.1016/j.bbamcr.2014.10.014  1
2015 Jolly MK, Boareto M, Huang B, Jia D, Lu M, Onuchic JN, Levine H, Ben-Jacob E. Implications of the hybrid epithelial/mesenchymal phenotype in metastasis Frontiers in Oncology. 5. DOI: 10.3389/fonc.2015.00155  1
2015 Hayes RL, Noel JK, Mandic A, Whitford PC, Sanbonmatsu KY, Mohanty U, Onuchic JN. Generalized Manning Condensation Model Captures the RNA Ion Atmosphere Physical Review Letters. 114. DOI: 10.1103/PhysRevLett.114.258105  1
2015 Jolly MK, Boareto M, Lu M, Onuchic JN, Clementi C, Ben-Jacob E. Operating principles of Notch-Delta-Jagged module of cell-cell communication New Journal of Physics. 17. DOI: 10.1088/1367-2630/17/5/055021  1
2014 Sun L, Noel JK, Sulkowska JI, Levine H, Onuchic JN. Connecting thermal and mechanical protein (un)folding landscapes. Biophysical Journal. 107: 2950-61. PMID 25517160 DOI: 10.1016/j.bpj.2014.10.021  1
2014 Ben-Jacob E, Lu M, Schultz D, Onuchic JN. The physics of bacterial decision making. Frontiers in Cellular and Infection Microbiology. 4: 154. PMID 25401094 DOI: 10.3389/fcimb.2014.00154  0.68
2014 Onuchic JN. Physics transforming the life sciences. Physical Biology. 11: 053006. PMID 25293472 DOI: 10.1088/1478-3975/11/5/053006  1
2014 Lu M, Huang B, Hanash SM, Onuchic JN, Ben-Jacob E. Modeling putative therapeutic implications of exosome exchange between tumor and immune cells. Proceedings of the National Academy of Sciences of the United States of America. 111: E4165-74. PMID 25246552 DOI: 10.1073/pnas.1416745111  1
2014 Huang B, Lu M, Jolly MK, Tsarfaty I, Onuchic J, Ben-Jacob E. The three-way switch operation of Rac1/RhoA GTPase-based circuit controlling amoeboid-hybrid-mesenchymal transition. Scientific Reports. 4: 6449. PMID 25245029 DOI: 10.1038/srep06449  1
2014 Lu M, Jolly MK, Onuchic J, Ben-Jacob E. Toward decoding the principles of cancer metastasis circuits. Cancer Research. 74: 4574-87. PMID 25183783 DOI: 10.1158/0008-5472.CAN-13-3367  1
2014 Lu M, Onuchic J, Ben-Jacob E. Construction of an effective landscape for multistate genetic switches. Physical Review Letters. 113: 078102. PMID 25170733 DOI: 10.1103/PhysRevLett.113.078102  1
2014 Morcos F, Schafer NP, Cheng RR, Onuchic JN, Wolynes PG. Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection. Proceedings of the National Academy of Sciences of the United States of America. 111: 12408-13. PMID 25114242 DOI: 10.1073/pnas.1413575111  1
2014 Zimmermann J, Hayes RL, Basan M, Onuchic JN, Rappel WJ, Levine H. Intercellular stress reconstitution from traction force data. Biophysical Journal. 107: 548-54. PMID 25099794 DOI: 10.1016/j.bpj.2014.06.036  1
2014 Lin X, Eddy NR, Noel JK, Whitford PC, Wang Q, Ma J, Onuchic JN. Order and disorder control the functional rearrangement of influenza hemagglutinin. Proceedings of the National Academy of Sciences of the United States of America. 111: 12049-54. PMID 25082896 DOI: 10.1073/pnas.1412849111  1
2014 Haglund E, Sulkowska JI, Noel JK, Lammert H, Onuchic JN, Jennings PA. Pierced Lasso Bundles are a new class of knot-like motifs. Plos Computational Biology. 10: e1003613. PMID 24945798 DOI: 10.1371/journal.pcbi.1003613  1
2014 Tamir S, Rotem-Bamberger S, Katz C, Morcos F, Hailey KL, Zuris JA, Wang C, Conlan AR, Lipper CH, Paddock ML, Mittler R, Onuchic JN, Jennings PA, Friedler A, Nechushtai R. Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1. Proceedings of the National Academy of Sciences of the United States of America. 111: 5177-82. PMID 24706857 DOI: 10.1073/pnas.1403770111  0.48
2014 Hayes RL, Noel JK, Whitford PC, Mohanty U, Sanbonmatsu KY, Onuchic JN. Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches. Biophysical Journal. 106: 1508-19. PMID 24703312 DOI: 10.1016/j.bpj.2014.01.042  1
2014 Jana B, Morcos F, Onuchic JN. From structure to function: the convergence of structure based models and co-evolutionary information. Physical Chemistry Chemical Physics : Pccp. 16: 6496-507. PMID 24603809 DOI: 10.1039/c3cp55275f  1
2014 Morcos F, Hwa T, Onuchic JN, Weigt M. Direct coupling analysis for protein contact prediction. Methods in Molecular Biology (Clifton, N.J.). 1137: 55-70. PMID 24573474 DOI: 10.1007/978-1-4939-0366-5_5  1
2014 Cheng RR, Morcos F, Levine H, Onuchic JN. Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proceedings of the National Academy of Sciences of the United States of America. 111: E563-71. PMID 24449878 DOI: 10.1073/pnas.1323734111  1
2014 van der Linden MG, Ferreira DC, de Oliveira LC, Onuchic JN, de Araújo AF. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure. Proteins. 82: 1186-99. PMID 24356941 DOI: 10.1002/prot.24483  1
2013 Morcos F, Jana B, Hwa T, Onuchic JN. Coevolutionary signals across protein lineages help capture multiple protein conformations. Proceedings of the National Academy of Sciences of the United States of America. 110: 20533-8. PMID 24297889 DOI: 10.1073/pnas.1315625110  1
2013 Lu M, Jolly MK, Levine H, Onuchic JN, Ben-Jacob E. MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination. Proceedings of the National Academy of Sciences of the United States of America. 110: 18144-9. PMID 24154725 DOI: 10.1073/pnas.1318192110  1
2013 Eaton WA, Gruebele M, Lubchenko V, Onuchic JN. Tribute to Peter G. Wolynes. The Journal of Physical Chemistry. B. 117: 12669-71. PMID 24152073 DOI: 10.1021/jp406995z  1
2013 Capraro DT, Lammert H, Heidary DK, Roy M, Gross LA, Onuchic JN, Jennings PA. Altered backbone and side-chain interactions result in route heterogeneity during the folding of interleukin-1β (IL-1β). Biophysical Journal. 105: 975-83. PMID 23972849 DOI: 10.1016/j.bpj.2013.06.019  1
2013 Sohn YS, Tamir S, Song L, Michaeli D, Matouk I, Conlan AR, Harir Y, Holt SH, Shulaev V, Paddock ML, Hochberg A, Cabanchick IZ, Onuchic JN, Jennings PA, Nechushtai R, et al. NAF-1 and mitoNEET are central to human breast cancer proliferation by maintaining mitochondrial homeostasis and promoting tumor growth. Proceedings of the National Academy of Sciences of the United States of America. 110: 14676-81. PMID 23959881 DOI: 10.1073/pnas.1313198110  1
2013 Lu M, Jolly MK, Gomoto R, Huang B, Onuchic J, Ben-Jacob E. Tristability in cancer-associated microRNA-TF chimera toggle switch. The Journal of Physical Chemistry. B. 117: 13164-74. PMID 23679052 DOI: 10.1021/jp403156m  1
2013 Schultz D, Lu M, Stavropoulos T, Onuchic J, Ben-Jacob E. Turning oscillations into opportunities: lessons from a bacterial decision gate. Scientific Reports. 3: 1668. PMID 23591544 DOI: 10.1038/srep01668  1
2013 Andrews BT, Capraro DT, Sulkowska JI, Onuchic JN, Jennings PA. Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins. The Journal of Physical Chemistry Letters. 4: 180-188. PMID 23525263 DOI: 10.1021/jz301893w  1
2013 Su?kowska JI, Noel JK, Ramírez-Sarmiento CA, Rawdon EJ, Millett KC, Onuchic JN. Knotting pathways in proteins. Biochemical Society Transactions. 41: 523-7. PMID 23514147 DOI: 10.1042/BST20120342  1
2013 Bai F, Xu Y, Chen J, Liu Q, Gu J, Wang X, Ma J, Li H, Onuchic JN, Jiang H. Free energy landscape for the binding process of Huperzine A to acetylcholinesterase. Proceedings of the National Academy of Sciences of the United States of America. 110: 4273-8. PMID 23440190 DOI: 10.1073/pnas.1301814110  1
2013 Onuchic JN, Jennings PA, Ben-Jacob E. Learning from cancer how to defeat bacteria. Proceedings of the National Academy of Sciences of the United States of America. 110: 3212-3. PMID 23407166 DOI: 10.1073/pnas.1222882110  1
2013 Baxter EL, Zuris JA, Wang C, Vo PL, Axelrod HL, Cohen AE, Paddock ML, Nechushtai R, Onuchic JN, Jennings PA. Allosteric control in a metalloprotein dramatically alters function. Proceedings of the National Academy of Sciences of the United States of America. 110: 948-53. PMID 23271805 DOI: 10.1073/pnas.1208286110  1
2013 Noel JK, Onuchic JN, Sulkowska JI. Knotting a protein in explicit solvent Journal of Physical Chemistry Letters. 4: 3570-3573. DOI: 10.1021/jz401842f  1
2012 Jana B, Hyeon C, Onuchic JN. The origin of minus-end directionality and mechanochemistry of Ncd motors. Plos Computational Biology. 8: e1002783. PMID 23166486 DOI: 10.1371/journal.pcbi.1002783  1
2012 Lammert H, Noel JK, Onuchic JN. The dominant folding route minimizes backbone distortion in SH3. Plos Computational Biology. 8: e1002776. PMID 23166485 DOI: 10.1371/journal.pcbi.1002776  1
2012 Schultz D, Onuchic JN, Ben-Jacob E. Turning death into creative force during biofilm engineering. Proceedings of the National Academy of Sciences of the United States of America. 109: 18633-4. PMID 23118336 DOI: 10.1073/pnas.1215227109  1
2012 Haglund E, SuÅ‚kowska JI, He Z, Feng GS, Jennings PA, Onuchic JN. The unique cysteine knot regulates the pleotropic hormone leptin. Plos One. 7: e45654. PMID 23029163 DOI: 10.1371/journal.pone.0045654  1
2012 Jamros MA, Oliveira LC, Whitford PC, Onuchic JN, Adams JA, Jennings PA. Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinase function. Plos Computational Biology. 8: e1002695. PMID 23028292 DOI: 10.1371/journal.pcbi.1002695  1
2012 Wang J, Oliveira RJ, Chu X, Whitford PC, Chahine J, Han W, Wang E, Onuchic JN, Leite VB. Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 109: 15763-8. PMID 23019359 DOI: 10.1073/pnas.1212842109  1
2012 Beratan DN, Onuchic JN. Redox redux. Physical Chemistry Chemical Physics : Pccp. 14: 13728. PMID 22960628 DOI: 10.1039/c2cp90148j  1
2012 Su?kowska JI, Noel JK, Onuchic JN. Energy landscape of knotted protein folding. Proceedings of the National Academy of Sciences of the United States of America. 109: 17783-8. PMID 22891304 DOI: 10.1073/pnas.1201804109  1
2012 Whitford PC, Sanbonmatsu KY, Onuchic JN. Biomolecular dynamics: order-disorder transitions and energy landscapes. Reports On Progress in Physics. Physical Society (Great Britain). 75: 076601. PMID 22790780 DOI: 10.1088/0034-4885/75/7/076601  1
2012 Capraro DT, Gosavi S, Roy M, Onuchic JN, Jennings PA. Folding circular permutants of IL-1β: route selection driven by functional frustration. Plos One. 7: e38512. PMID 22693643 DOI: 10.1371/journal.pone.0038512  1
2012 Su?kowska JI, Morcos F, Weigt M, Hwa T, Onuchic JN. Genomics-aided structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 109: 10340-5. PMID 22691493 DOI: 10.1073/pnas.1207864109  1
2012 SuÅ‚kowska JI, Rawdon EJ, Millett KC, Onuchic JN, Stasiak A. Conservation of complex knotting and slipknotting patterns in proteins. Proceedings of the National Academy of Sciences of the United States of America. 109: E1715-23. PMID 22685208 DOI: 10.1073/pnas.1205918109  1
2012 Hayes RL, Noel JK, Mohanty U, Whitford PC, Hennelly SP, Onuchic JN, Sanbonmatsu KY. Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch. Journal of the American Chemical Society. 134: 12043-53. PMID 22612276 DOI: 10.1021/ja301454u  1
2012 Noel JK, Whitford PC, Onuchic JN. The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function. The Journal of Physical Chemistry. B. 116: 8692-702. PMID 22536820 DOI: 10.1021/jp300852d  1
2012 Noel JK, Schug A, Verma A, Wenzel W, Garcia AE, Onuchic JN. Mirror images as naturally competing conformations in protein folding. The Journal of Physical Chemistry. B. 116: 6880-8. PMID 22497217 DOI: 10.1021/jp212623d  1
2012 Baxter EL, Jennings PA, Onuchic JN. Strand swapping regulates the iron-sulfur cluster in the diabetes drug target mitoNEET. Proceedings of the National Academy of Sciences of the United States of America. 109: 1955-60. PMID 22308404 DOI: 10.1073/pnas.1116369109  1
2012 Capraro DT, Roy M, Onuchic JN, Gosavi S, Jennings PA. β-Bulge triggers route-switching on the functional landscape of interleukin-1β. Proceedings of the National Academy of Sciences of the United States of America. 109: 1490-3. PMID 22307602 DOI: 10.1073/pnas.1114430109  1
2012 Singh JP, Whitford PC, Hayre NR, Onuchic J, Cox DL. Massive conformation change in the prion protein: Using dual-basin structure-based models to find misfolding pathways. Proteins. 80: 1299-307. PMID 22274922 DOI: 10.1002/prot.24026  1
2012 Lammert H, Wolynes PG, Onuchic JN. The role of atomic level steric effects and attractive forces in protein folding. Proteins. 80: 362-73. PMID 22081451 DOI: 10.1002/prot.23187  1
2011 Hyeon C, Onuchic JN. A structural perspective on the dynamics of kinesin motors. Biophysical Journal. 101: 2749-59. PMID 22261064 DOI: 10.1016/j.bpj.2011.10.037  1
2011 Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proceedings of the National Academy of Sciences of the United States of America. 108: E1293-301. PMID 22106262 DOI: 10.1073/pnas.1111471108  1
2011 Whitford PC, Ahmed A, Yu Y, Hennelly SP, Tama F, Spahn CM, Onuchic JN, Sanbonmatsu KY. Excited states of ribosome translocation revealed through integrative molecular modeling. Proceedings of the National Academy of Sciences of the United States of America. 108: 18943-8. PMID 22080606 DOI: 10.1073/pnas.1108363108  1
2011 Zuris JA, Harir Y, Conlan AR, Shvartsman M, Michaeli D, Tamir S, Paddock ML, Onuchic JN, Mittler R, Cabantchik ZI, Jennings PA, Nechushtai R. Facile transfer of [2Fe-2S] clusters from the diabetes drug target mitoNEET to an apo-acceptor protein. Proceedings of the National Academy of Sciences of the United States of America. 108: 13047-52. PMID 21788481 DOI: 10.1073/pnas.1109986108  1
2011 Suzuki Y, Noel JK, Onuchic JN. A semi-analytical description of protein folding that incorporates detailed geometrical information. The Journal of Chemical Physics. 134: 245101. PMID 21721664 DOI: 10.1063/1.3599473  1
2011 Ferreira FM, Oliveira LC, Germino GG, Onuchic JN, Onuchic LF. Macromolecular assembly of polycystin-2 intracytosolic C-terminal domain. Proceedings of the National Academy of Sciences of the United States of America. 108: 9833-8. PMID 21622852 DOI: 10.1073/pnas.1106766108  1
2011 Baxter EL, Jennings PA, Onuchic JN. Interdomain communication revealed in the diabetes drug target mitoNEET. Proceedings of the National Academy of Sciences of the United States of America. 108: 5266-71. PMID 21402934 DOI: 10.1073/pnas.1017604108  1
2011 Nechushtai R, Lammert H, Michaeli D, Eisenberg-Domovich Y, Zuris JA, Luca MA, Capraro DT, Fish A, Shimshon O, Roy M, Schug A, Whitford PC, Livnah O, Onuchic JN, Jennings PA. Allostery in the ferredoxin protein motif does not involve a conformational switch. Proceedings of the National Academy of Sciences of the United States of America. 108: 2240-5. PMID 21266547 DOI: 10.1073/pnas.1019502108  1
2010 Ratje AH, Loerke J, Mikolajka A, Brünner M, Hildebrand PW, Starosta AL, Dönhöfer A, Connell SR, Fucini P, Mielke T, Whitford PC, Onuchic JN, Yu Y, Sanbonmatsu KY, Hartmann RK, et al. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature. 468: 713-6. PMID 21124459 DOI: 10.1038/nature09547  1
2010 Schug A, Onuchic JN. From protein folding to protein function and biomolecular binding by energy landscape theory. Current Opinion in Pharmacology. 10: 709-14. PMID 20951644 DOI: 10.1016/j.coph.2010.09.012  1
2010 Schug A, Weigt M, Hoch JA, Onuchic JN, Hwa T, Szurmant H. Computational modeling of phosphotransfer complexes in two-component signaling. Methods in Enzymology. 471: 43-58. PMID 20946841 DOI: 10.1016/S0076-6879(10)71003-X  1
2010 Whitford PC, Onuchic JN, Sanbonmatsu KY. Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome. Journal of the American Chemical Society. 132: 13170-1. PMID 20806913 DOI: 10.1021/ja1061399  1
2010 Jamros MA, Oliveira LC, Whitford PC, Onuchic JN, Adams JA, Blumenthal DK, Jennings PA. Proteins at work: a combined small angle X-RAY scattering and theoretical determination of the multiple structures involved on the protein kinase functional landscape. The Journal of Biological Chemistry. 285: 36121-8. PMID 20801888 DOI: 10.1074/jbc.M110.116947  1
2010 Noel JK, Su?kowska JI, Onuchic JN. Slipknotting upon native-like loop formation in a trefoil knot protein. Proceedings of the National Academy of Sciences of the United States of America. 107: 15403-8. PMID 20702769 DOI: 10.1073/pnas.1009522107  1
2010 Oliveira RJ, Whitford PC, Chahine J, Wang J, Onuchic JN, Leite VB. The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding. Biophysical Journal. 99: 600-8. PMID 20643080 DOI: 10.1016/j.bpj.2010.04.041  1
2010 Noel JK, Whitford PC, Sanbonmatsu KY, Onuchic JN. SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Research. 38: W657-61. PMID 20525782 DOI: 10.1093/nar/gkq498  1
2010 Whitford PC, Geggier P, Altman RB, Blanchard SC, Onuchic JN, Sanbonmatsu KY. Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. Rna (New York, N.Y.). 16: 1196-204. PMID 20427512 DOI: 10.1261/rna.2035410  1
2010 Bölinger D, Su?kowska JI, Hsu HP, Mirny LA, Kardar M, Onuchic JN, Virnau P. A Stevedore's protein knot. Plos Computational Biology. 6: e1000731. PMID 20369018 DOI: 10.1371/journal.pcbi.1000731  1
2009 Su?kowska JI, Su?kowski P, Onuchic JN. Jamming proteins with slipknots and their free energy landscape. Physical Review Letters. 103: 268103. PMID 20366349 DOI: 10.1103/PhysRevLett.103.268103  1
2009 Schug A, Weigt M, Onuchic JN, Hwa T, Szurmant H. High-resolution protein complexes from integrating genomic information with molecular simulation. Proceedings of the National Academy of Sciences of the United States of America. 106: 22124-9. PMID 20018738 DOI: 10.1073/pnas.0912100106  1
2009 Schultz D, Wolynes PG, Ben Jacob E, Onuchic JN. Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America. 106: 21027-34. PMID 19995980 DOI: 10.1073/pnas.0912185106  1
2009 Pereira de Araujo AF, Onuchic JN. A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins. Proceedings of the National Academy of Sciences of the United States of America. 106: 19001-4. PMID 19858496 DOI: 10.1073/pnas.0910851106  1
2009 Lammert H, Schug A, Onuchic JN. Robustness and generalization of structure-based models for protein folding and function. Proteins. 77: 881-91. PMID 19626713 DOI: 10.1002/prot.22511  1
2009 Hyeon C, Klumpp S, Onuchic JN. Kinesin's backsteps under mechanical load. Physical Chemistry Chemical Physics : Pccp. 11: 4899-910. PMID 19506765 DOI: 10.1039/b903536b  1
2009 Gambin Y, Schug A, Lemke EA, Lavinder JJ, Ferreon AC, Magliery TJ, Onuchic JN, Deniz AA. Direct single-molecule observation of a protein living in two opposed native structures. Proceedings of the National Academy of Sciences of the United States of America. 106: 10153-8. PMID 19506258 DOI: 10.1073/pnas.0904461106  1
2009 Sułkowska JI, Sułkowski P, Onuchic J. Dodging the crisis of folding proteins with knots. Proceedings of the National Academy of Sciences of the United States of America. 106: 3119-24. PMID 19211785 DOI: 10.1073/pnas.0811147106  1
2009 Hyeon C, Jennings PA, Adams JA, Onuchic JN. Ligand-induced global transitions in the catalytic domain of protein kinase A. Proceedings of the National Academy of Sciences of the United States of America. 106: 3023-8. PMID 19204278 DOI: 10.1073/pnas.0813266106  1
2009 Whitford PC, Schug A, Saunders J, Hennelly SP, Onuchic JN, Sanbonmatsu KY. Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function. Biophysical Journal. 96: L7-9. PMID 19167285 DOI: 10.1016/j.bpj.2008.10.033  1
2009 Whitford PC, Noel JK, Gosavi S, Schug A, Sanbonmatsu KY, Onuchic JN. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields. Proteins. 75: 430-41. PMID 18837035 DOI: 10.1002/prot.22253  1
2008 Whitford PC, Onuchic JN, Wolynes PG. Energy landscape along an enzymatic reaction trajectory: hinges or cracks? Hfsp Journal. 2: 61-4. PMID 19404472 DOI: 10.2976/1.2894846  1
2008 Schultz D, Walczak AM, Onuchic JN, Wolynes PG. Extinction and resurrection in gene networks. Proceedings of the National Academy of Sciences of the United States of America. 105: 19165-70. PMID 19033463 DOI: 10.1073/pnas.0810366105  1
2008 Capraro DT, Roy M, Onuchic JN, Jennings PA. Backtracking on the folding landscape of the beta-trefoil protein interleukin-1beta? Proceedings of the National Academy of Sciences of the United States of America. 105: 14844-8. PMID 18806223 DOI: 10.1073/pnas.0807812105  1
2008 Liu J, Desai A, Onuchic JN, Hwa T. An integrated mechanobiochemical feedback mechanism describes chromosome motility from prometaphase to anaphase in mitosis. Proceedings of the National Academy of Sciences of the United States of America. 105: 13752-7. PMID 18780795 DOI: 10.1073/pnas.0807007105  1
2008 Andrews BT, Gosavi S, Finke JM, Onuchic JN, Jennings PA. The dual-basin landscape in GFP folding. Proceedings of the National Academy of Sciences of the United States of America. 105: 12283-8. PMID 18713871 DOI: 10.1073/pnas.0804039105  1
2008 Gosavi S, Whitford PC, Jennings PA, Onuchic JN. Extracting function from a beta-trefoil folding motif. Proceedings of the National Academy of Sciences of the United States of America. 105: 10384-9. PMID 18650393 DOI: 10.1073/pnas.0801343105  1
2008 Oliveira LC, Schug A, Onuchic JN. Geometrical features of the protein folding mechanism are a robust property of the energy landscape: a detailed investigation of several reduced models. The Journal of Physical Chemistry. B. 112: 6131-6. PMID 18251535 DOI: 10.1021/jp0769835  1
2008 Suzuki Y, Noel JK, Onuchic JN. An analytical study of the interplay between geometrical and energetic effects in protein folding. The Journal of Chemical Physics. 128: 025101. PMID 18205476 DOI: 10.1063/1.2812956  1
2008 Whitford PC, Gosavi S, Onuchic JN. Conformational transitions in adenylate kinase. Allosteric communication reduces misligation. The Journal of Biological Chemistry. 283: 2042-8. PMID 17998210 DOI: 10.1074/jbc.M707632200  1
2008 Onuchic JN. Special issue on protein folding: Experimental and theoretical approaches Hfsp Journal. 2: 295-296. DOI: 10.2976/1.3023645  1
2008 Gosavi S, Whitford PC, Jennings PA, Onuchic JN. Extracting function from a β-trefoil folding motif (Proceedings of the National Academy of Sciences of the United States of America (2008) 105, 30 (11384-10389) DOI: 10.1073/pnas.0801343105)) Proceedings of the National Academy of Sciences of the United States of America. 105: 16057. DOI: 10.1073/pnas.0808551105  1
2008 Onuchic JN, Kobayashi C, Baldridge KK. Quantum tunneling in biological reactions: The interplay between theory and experiments Journal of the Brazilian Chemical Society. 19: 206-210.  1
2007 Schug A, Whitford PC, Levy Y, Onuchic JN. Mutations as trapdoors to two competing native conformations of the Rop-dimer. Proceedings of the National Academy of Sciences of the United States of America. 104: 17674-9. PMID 17968016 DOI: 10.1073/pnas.0706077104  1
2007 Schultz D, Ben Jacob E, Onuchic JN, Wolynes PG. Molecular level stochastic model for competence cycles in Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America. 104: 17582-7. PMID 17962411 DOI: 10.1073/pnas.0707965104  1
2007 Hyeon C, Onuchic JN. Mechanical control of the directional stepping dynamics of the kinesin motor. Proceedings of the National Academy of Sciences of the United States of America. 104: 17382-7. PMID 17959770 DOI: 10.1073/pnas.0708828104  1
2007 Liu J, Desai A, Onuchic JN, Hwa T. A mechanobiochemical mechanism for monooriented chromosome oscillation in mitosis. Proceedings of the National Academy of Sciences of the United States of America. 104: 16104-9. PMID 17911248 DOI: 10.1073/pnas.0707689104  1
2007 Yang S, Onuchic JN, García AE, Levine H. Folding time predictions from all-atom replica exchange simulations. Journal of Molecular Biology. 372: 756-63. PMID 17681536 DOI: 10.1016/j.jmb.2007.07.010  1
2007 Schultz D, Onuchic JN, Wolynes PG. Understanding stochastic simulations of the smallest genetic networks. The Journal of Chemical Physics. 126: 245102. PMID 17614590 DOI: 10.1063/1.2741544  1
2007 Finke JM, Jennings PA, Lee JC, Onuchic JN, Winkler JR. Equilibrium unfolding of the poly(glutamic acid)20 helix. Biopolymers. 86: 193-211. PMID 17370320 DOI: 10.1002/bip.20719  1
2007 Hyeon C, Onuchic JN. Internal strain regulates the nucleotide binding site of the kinesin leading head. Proceedings of the National Academy of Sciences of the United States of America. 104: 2175-80. PMID 17287347 DOI: 10.1073/pnas.0610939104  1
2007 Levy Y, Onuchic JN, Wolynes PG. Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition. Journal of the American Chemical Society. 129: 738-9. PMID 17243791 DOI: 10.1021/ja065531n  1
2007 Whitford PC, Miyashita O, Levy Y, Onuchic JN. Conformational transitions of adenylate kinase: switching by cracking. Journal of Molecular Biology. 366: 1661-71. PMID 17217965 DOI: 10.1016/j.jmb.2006.11.085  1
2007 Mills JE, Whitford PC, Shaffer J, Onuchic JN, Adams JA, Jennings PA. A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity. Journal of Molecular Biology. 365: 1460-8. PMID 17137590 DOI: 10.1016/j.jmb.2006.10.076  1
2006 Liu J, Onuchic JN. A driving and coupling "Pac-Man" mechanism for chromosome poleward translocation in anaphase A. Proceedings of the National Academy of Sciences of the United States of America. 103: 18432-7. PMID 17130449 DOI: 10.1073/pnas.0608962103  1
2006 Simler BR, Levy Y, Onuchic JN, Matthews CR. The folding energy landscape of the dimerization domain of Escherichia coli Trp repressor: a joint experimental and theoretical investigation. Journal of Molecular Biology. 363: 262-78. PMID 16956620 DOI: 10.1016/j.jmb.2006.07.080  1
2006 Yang S, Onuchic JN, Levine H. Effective stochastic dynamics on a protein folding energy landscape. The Journal of Chemical Physics. 125: 054910. PMID 16942260 DOI: 10.1063/1.2229206  1
2006 Okazaki K, Koga N, Takada S, Onuchic JN, Wolynes PG. Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 103: 11844-9. PMID 16877541 DOI: 10.1073/pnas.0604375103  1
2006 Onuchic JN, Kobayashi C, Miyashita O, Jennings P, Baldridge KK. Exploring biomolecular machines: energy landscape control of biological reactions. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 1439-43. PMID 16873130 DOI: 10.1098/rstb.2006.1876  1
2006 Chavez LL, Gosavi S, Jennings PA, Onuchic JN. Multiple routes lead to the native state in the energy landscape of the beta-trefoil family. Proceedings of the National Academy of Sciences of the United States of America. 103: 10254-8. PMID 16801558 DOI: 10.1073/pnas.0510110103  1
2006 Levy Y, Onuchic JN. Water mediation in protein folding and molecular recognition. Annual Review of Biophysics and Biomolecular Structure. 35: 389-415. PMID 16689642 DOI: 10.1146/annurev.biophys.35.040405.102134  1
2006 Levy Y, Onuchic JN. Mechanisms of protein assembly: lessons from minimalist models. Accounts of Chemical Research. 39: 135-42. PMID 16489733 DOI: 10.1021/ar040204a  1
2006 Gosavi S, Chavez LL, Jennings PA, Onuchic JN. Topological frustration and the folding of interleukin-1 beta. Journal of Molecular Biology. 357: 986-96. PMID 16469330 DOI: 10.1016/j.jmb.2005.11.074  1
2005 Suzuki Y, Onuchic JN. Modeling the interplay between geometrical and energetic effects in protein folding. The Journal of Physical Chemistry. B. 109: 16503-10. PMID 16853098 DOI: 10.1021/jp0512863  1
2005 Miyashita O, Wolynes PG, Onuchic JN. Simple energy landscape model for the kinetics of functional transitions in proteins. The Journal of Physical Chemistry. B. 109: 1959-69. PMID 16851180 DOI: 10.1021/jp046736q  1
2005 Hornos JE, Schultz D, Innocentini GC, Wang J, Walczak AM, Onuchic JN, Wolynes PG. Self-regulating gene: an exact solution. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 051907. PMID 16383645 DOI: 10.1103/PhysRevE.72.051907  1
2005 Walczak AM, Onuchic JN, Wolynes PG. Absolute rate theories of epigenetic stability. Proceedings of the National Academy of Sciences of the United States of America. 102: 18926-31. PMID 16361441 DOI: 10.1073/pnas.0509547102  1
2005 Yang S, Levine H, Onuchic JN, Cox DL. Structure of infectious prions: stabilization by domain swapping. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 19: 1778-82. PMID 16260647 DOI: 10.1096/fj.05-4067hyp  1
2005 Cho SS, Levy Y, Onuchic JN, Wolynes PG. Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation. Physical Biology. 2: S44-55. PMID 16204848 DOI: 10.1088/1478-3975/2/2/S05  1
2005 Yang S, Levine H, Onuchic JN. Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration. Journal of Molecular Biology. 352: 202-11. PMID 16061250 DOI: 10.1016/j.jmb.2005.06.062  1
2005 Wong L, Lieser SA, Miyashita O, Miller M, Tasken K, Onuchic JN, Adams JA, Woods VL, Jennings PA. Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation. Journal of Molecular Biology. 351: 131-43. PMID 16002086 DOI: 10.1016/j.jmb.2005.05.042  1
2005 Garcia AE, Onuchic JN. Folding a protein in the computer: reality or hope? Structure (London, England : 1993). 13: 497-8. PMID 15837185 DOI: 10.1016/j.str.2005.03.005  1
2005 Finke JM, Onuchic JN. Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape. Biophysical Journal. 89: 488-505. PMID 15833999 DOI: 10.1529/biophysj.105.059147  1
2005 Roy M, Chavez LL, Finke JM, Heidary DK, Onuchic JN, Jennings PA. The native energy landscape for interleukin-1beta. Modulation of the population ensemble through native-state topology. Journal of Molecular Biology. 348: 335-47. PMID 15811372 DOI: 10.1016/j.jmb.2005.02.059  1
2005 Miyashita O, Okamura MY, Onuchic JN. Interprotein electron transfer from cytochrome c2 to photosynthetic reaction center: Tunneling across an aqueous interface Proceedings of the National Academy of Sciences of the United States of America. 102: 3558-3563. PMID 15738426 DOI: 10.1073/pnas.0409600102  1
2005 Levy Y, Cho SS, Shen T, Onuchic JN, Wolynes PG. Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. Proceedings of the National Academy of Sciences of the United States of America. 102: 2373-8. PMID 15701699 DOI: 10.1073/pnas.0409572102  1
2005 Levy Y, Cho SS, Onuchic JN, Wolynes PG. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. Journal of Molecular Biology. 346: 1121-45. PMID 15701522 DOI: 10.1016/j.jmb.2004.12.021  1
2004 Miyashita O, Onuchic JN, Okamura MY. Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center Proceedings of the National Academy of Sciences of the United States of America. 101: 16174-16179. PMID 15520377 DOI: 10.1073/pnas.0405745101  1
2004 Leite VBP, Onuchic JN, Stell G, Wang J. Probing the kinetics of single molecule protein folding Biophysical Journal. 87: 3633-3641. PMID 15465871 DOI: 10.1529/biophysj.104.046243  1
2004 Yang S, Cho SS, Levy Y, Cheung MS, Levine H, Wolynes PG, Onuchic JN. Domain swapping is a consequence of minimal frustration. Proceedings of the National Academy of Sciences of the United States of America. 101: 13786-91. PMID 15361578 DOI: 10.1073/pnas.0403724101  1
2004 Finke JM, Cheung MS, Onuchic JN. A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory. Biophysical Journal. 87: 1900-18. PMID 15345567 DOI: 10.1529/biophysj.104.041533  1
2004 Wong L, Lieser S, Chie-Leon B, Miyashita O, Aubol B, Shaffer J, Onuchic JN, Jennings PA, Woods VL, Adams JA. Dynamic coupling between the SH2 domain and active site of the COOH terminal Src kinase, Csk. Journal of Molecular Biology. 341: 93-106. PMID 15312765 DOI: 10.1016/j.jmb.2004.05.060  1
2004 Chavez LL, Onuchic JN, Clementi C. Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. Journal of the American Chemical Society. 126: 8426-32. PMID 15237999 DOI: 10.1021/ja049510+  1
2004 Stoycheva AD, Brooks CL, Onuchic JN. Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model. Journal of Molecular Biology. 340: 571-85. PMID 15210355 DOI: 10.1016/j.jmb.2004.04.073  1
2004 Levy Y, Caflisch A, Onuchic JN, Wolynes PG. The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations. Journal of Molecular Biology. 340: 67-79. PMID 15184023 DOI: 10.1016/j.jmb.2004.04.028  1
2004 Onuchic JN, Wolynes PG. Theory of protein folding. Current Opinion in Structural Biology. 14: 70-5. PMID 15102452 DOI: 10.1016/j.sbi.2004.01.009  1
2004 Levy Y, Onuchic JN. Water and proteins: a love-hate relationship. Proceedings of the National Academy of Sciences of the United States of America. 101: 3325-6. PMID 14993602 DOI: 10.1073/pnas.0400157101  1
2004 Tan ML, Balabin I, Onuchic JN. Dynamics of electron transfer pathways in cytochrome C oxidase. Biophysical Journal. 86: 1813-9. PMID 14990507 DOI: 10.1016/S0006-3495(04)74248-4  1
2004 Fernández-Escamilla AM, Cheung MS, Vega MC, Wilmanns M, Onuchic JN, Serrano L. Solvation in protein folding analysis: combination of theoretical and experimental approaches. Proceedings of the National Academy of Sciences of the United States of America. 101: 2834-9. PMID 14978284 DOI: 10.1073/pnas.0304180101  1
2004 Levy Y, Wolynes PG, Onuchic JN. Protein topology determines binding mechanism. Proceedings of the National Academy of Sciences of the United States of America. 101: 511-6. PMID 14694192 DOI: 10.1073/pnas.2534828100  1
2004 Levy Y, Papoian GA, Onuchic JN, Wolynes PG. Energy landscape analysis of protein dimers Israel Journal of Chemistry. 44: 281-297. DOI: 10.1560/XGCB-WUHN-JRJC-BV0Y  1
2004 Cheung MS, Chavez LL, Onuchic JN. The energy landscape for protein folding and possible connections to function Polymer. 45: 547-555. DOI: 10.1016/j.polymer.2003.10.082  1
2003 García AE, Onuchic JN. Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proceedings of the National Academy of Sciences of the United States of America. 100: 13898-903. PMID 14623983 DOI: 10.1073/pnas.2335541100  1
2003 Miyashita O, Onuchic JN, Wolynes PG. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proceedings of the National Academy of Sciences of the United States of America. 100: 12570-5. PMID 14566052 DOI: 10.1073/pnas.2135471100  1
2003 Miyashita O, Onuchic JN, Okamura MY. Continuum electrostatic model for the binding of cytochrome c2 to the photosynthetic reaction center from Rhodobacter sphaeroides Biochemistry. 42: 11651-11660. PMID 14529275 DOI: 10.1021/bi0350250  1
2003 Clementi C, García AE, Onuchic JN. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. Journal of Molecular Biology. 326: 933-54. PMID 12581651 DOI: 10.1016/S0022-2836(02)01379-7  1
2003 Stoycheva AD, Onuchic JN, Brooks CL. Effect of gatekeepers on the early folding kinetics of a model β-barrel protein Journal of Chemical Physics. 119: 5722-5729. DOI: 10.1063/1.1599281  1
2003 Kobayashi C, Baldridge K, Onuchic JN. Multiple versus single pathways in electron transfer in proteins: Influence of protein dynamics and hydrogen bonds Journal of Chemical Physics. 119: 3550-3558. DOI: 10.1063/1.1588293  1
2003 Miyashita O, Okamura MY, Onuchic JN. Theoretical understanding of the interprotein electron transfer between cytochrome c2 and the photosynthetic reaction center Journal of Physical Chemistry B. 107: 1230-1241. DOI: 10.1021/jp026753k  1
2003 Cheung MS, Finke JM, Callahan B, Onuchic JN. Exploring the interplay between topology and secondary structural formation in the protein folding problem Journal of Physical Chemistry B. 107: 11193-11200.  1
2002 Miyashita O, Axelrod HL, Onuchic JN. Different scenarios for inter-protein electron tunneling: the effect of water-mediated pathways. Journal of Biological Physics. 28: 383-94. PMID 23345783 DOI: 10.1023/A:1020308521041  1
2002 Plotkin SS, Onuchic JN. Understanding protein folding with energy landscape theory. Part II: Quantitative aspects. Quarterly Reviews of Biophysics. 35: 205-86. PMID 12599750 DOI: 10.1017/S0033583502003785  1
2002 Shea JE, Onuchic JN, Brooks CL. Probing the folding free energy landscape of the Src-SH3 protein domain. Proceedings of the National Academy of Sciences of the United States of America. 99: 16064-8. PMID 12446834 DOI: 10.1073/pnas.242293099  1
2002 Plotkin SS, Onuchic JN. Understanding protein folding with energy landscape theory. Part I: Basic concepts. Quarterly Reviews of Biophysics. 35: 111-67. PMID 12197302 DOI: 10.1017/S0033583502003761  1
2002 Chahine J, Nymeyer H, Leite VB, Socci ND, Onuchic JN. Specific and nonspecific collapse in protein folding funnels. Physical Review Letters. 88: 168101. PMID 11955268  1
2002 Cheung MS, García AE, Onuchic JN. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proceedings of the National Academy of Sciences of the United States of America. 99: 685-90. PMID 11805324 DOI: 10.1073/pnas.022387699  1
2002 Tanimura Y, Leite VBP, Onuchic JN. The energy landscape for solvent dynamics in electron transfer reactions: A minimalist model Journal of Chemical Physics. 117: 2172-2179. DOI: 10.1063/1.1488588  1
2002 Plotkin SS, Onuchic JN. Structural and energetic heterogeneity in protein folding. I. Theory Journal of Chemical Physics. 116: 5263-5283. DOI: 10.1063/1.1449866  1
2001 Clementi C, Jennings PA, Onuchic JN. Prediction of folding mechanism for circular-permuted proteins. Journal of Molecular Biology. 311: 879-90. PMID 11518537 DOI: 10.1006/jmbi.2001.4871  1
2001 Brooks CL, Onuchic JN, Wales DJ. Statistical thermodynamics: Taking a walk on a landscape Science. 293: 612-613. PMID 11474087  1
2001 Hansmann UHE, Onuchic JN. Thermodynamics and kinetics of folding of a small peptide Journal of Chemical Physics. 115: 1601-1606. DOI: 10.1063/1.1379757  1
2000 Balabin IA, Onuchic JN. Dynamically controlled protein tunneling paths in photosynthetic reaction centers Science. 290: 114-117. PMID 11021791 DOI: 10.1126/science.290.5489.114  1
2000 Plotkin SS, Onuchic JN. Investigation of routes and funnels in protein folding by free energy functional methods Proceedings of the National Academy of Sciences of the United States of America. 97: 6509-6514. PMID 10841554 DOI: 10.1073/pnas.97.12.6509  1
2000 Clementi C, Jennings PA, Onuchic JN. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta. Proceedings of the National Academy of Sciences of the United States of America. 97: 5871-6. PMID 10811910 DOI: 10.1073/pnas.100547897  1
2000 Clementi C, Nymeyer H, Onuchic JN. 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. Journal of Molecular Biology. 298: 937-53. PMID 10801360 DOI: 10.1006/jmbi.2000.3693  1
2000 Onuchic JN, Nymeyer H, García AE, Chahine J, Socci ND. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. Advances in Protein Chemistry. 53: 87-152. PMID 10751944 DOI: 10.1016/S0065-3233(00)53003-4  1
2000 Nymeyer H, Socci ND, Onuchic JN. Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration. Proceedings of the National Academy of Sciences of the United States of America. 97: 634-9. PMID 10639131 DOI: 10.1073/pnas.97.2.634  1
2000 Shea JE, Onuchic JN, Brooks CL. Energetic frustration and the nature of the transition state in protein folding Journal of Chemical Physics. 113: 7663-7671. DOI: 10.1063/1.1313792  1
2000 García AE, Hillson N, Onuchic JN. Solvent effects on protein folding/unfolding Progress of Theoretical Physics Supplement. 282-291.  1
1999 Hillson N, Onuchic JN, Garcia AE. Pressure-induced protein-folding/unfolding kinetics Proceedings of the National Academy of Sciences of the United States of America. 96: 14848-14853. PMID 10611301 DOI: 10.1073/pnas.96.26.14848  1
1999 Shea JE, Onuchic JN, Brooks CL. Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A Proceedings of the National Academy of Sciences of the United States of America. 96: 12512-12517. PMID 10535953 DOI: 10.1073/pnas.96.22.12512  1
1999 Hansmann UHE, Okamoto Y, Onuchic JN. The folding funnel landscape for the peptide Met-enkephalin Proteins: Structure, Function and Genetics. 34: 472-483. PMID 10081960 DOI: 10.1002/(SICI)1097-0134(19990301)34:4<472::AID-PROT7>3.0.CO;2-X  1
1999 Socci ND, Onuchic JN, Wolynes PG. Stretching lattice models of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 96: 2031-5. PMID 10051589 DOI: 10.1073/pnas.96.5.2031  1
1999 Regan JJ, Onuchic JN. Electron-transfer tubes Advances in Chemical Physics. 107: 497-553.  1
1999 Onuchic JN, Wang J, Wolynes PG. Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions Chemical Physics. 247: 175-184.  1
1998 Brooks CL, Gruebele M, Onuchic JN, Wolynes PG. Chemical physics of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 95: 11037-8. PMID 9736683 DOI: 10.1073/pnas.95.19.11037  1
1998 Nelson ED, Onuchic JN. Proposed mechanism for stability of proteins to evolutionary mutations Proceedings of the National Academy of Sciences of the United States of America. 95: 10682-10686. PMID 9724764 DOI: 10.1073/pnas.95.18.10682  1
1998 Socci ND, Onuchic JN, Wolynes PG. Protein folding mechanisms and the multidimensional folding funnel. Proteins. 32: 136-58. PMID 9714155 DOI: 10.1002/(SICI)1097-0134(19980801)32:2<136::AID-PROT2>3.0.CO;2-J  1
1998 Nymeyer H, García AE, Onuchic JN. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proceedings of the National Academy of Sciences of the United States of America. 95: 5921-8. PMID 9600893 DOI: 10.1073/pnas.95.11.5921  1
1998 Regan JJ, Chang FK, Onuchic JN. Tubular breakdown of electron transfer in proteins Advances in Chemistry Series. 254: 111-129.  1
1998 Balabin IA, Onuchic JN. A new framework for electron-transfer calculations - Beyond the pathways-like models Journal of Physical Chemistry B. 102: 7497-7505.  1
1998 De Andrade PCP, Onuchic JN. Generalized pathway model to compute and analyze tunneling matrix elements in proteins Journal of Chemical Physics. 108: 4292-4298.  1
1997 Onuchic JN, Luthey-Schulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annual Review of Physical Chemistry. 48: 545-600. PMID 9348663 DOI: 10.1146/annurev.physchem.48.1.545  1
1997 Onuchic JN. Contacting the protein folding funnel with NMR Proceedings of the National Academy of Sciences of the United States of America. 94: 7129-7131. PMID 9207055 DOI: 10.1073/pnas.94.14.7129  1
1997 Socci ND, Nymeyer H, Onuchic JN. Exploring the protein folding funnel landscape Physica D: Nonlinear Phenomena. 107: 366-382.  1
1997 Pande VS, Onuchic JN. Electron transport in disordered polymeric and biological systems Physical Review Letters. 78: 146-149.  1
1997 Nelson ED, Teneyck LF, Onuchic JN. Symmetry and kinetic optimization of proteinlike heteropolymers Physical Review Letters. 79: 3534-3537.  1
1997 Aquino AJA, Beroza P, Reagan J, Onuchic JN. Estimating the effect of protein dynamics on electron transfer to the special pair in the photosynthetic reaction center Chemical Physics Letters. 275: 181-187.  1
1996 Nocek JM, Zhou JS, De Forest S, Priyadarshy S, Beratan DN, Onuchic JN, Hoffman BM. Theory and Practice of Electron Transfer within Proteinminus signProtein Complexes: Application to the Multidomain Binding of Cytochrome c by Cytochrome c Peroxidase. Chemical Reviews. 96: 2459-2490. PMID 11848833  0.96
1996 Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG. Protein folding funnels: the nature of the transition state ensemble. Folding & Design. 1: 441-50. PMID 9080190 DOI: 10.1016/S1359-0278(96)00060-0  1
1996 Wolynes PG, Luthey-Schulten Z, Onuchic JN. Fast-folding experiments and the topography of protein folding energy landscapes Chemistry and Biology. 3: 425-432. PMID 8807873  1
1996 Socci ND, Onuchic JN, Wolynes PG. Diffusive dynamics of the reaction coordinate for protein folding funnels Journal of Chemical Physics. 104: 5860-5868.  1
1996 Nocek JM, Zhou JS, De Forest S, Priyadarshy S, Beratan DN, Onuchic JN, Huffman BM. Theory and practice of electron transfer within protein-protein complexes: Application to the multidomain binding of cytochrome c by cytochrome c peroxidase Chemical Reviews. 96: 2459-2489.  1
1988 Hopfield JJ, Onuchic JN, Beratan DN. A molecular shift register based on electron transfer. Science (New York, N.Y.). 241: 817-20. PMID 17829175 DOI: 10.1126/science.241.4867.817  1
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