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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
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Year Citation  Score
2023 Ruben BS, Brahmachari S, Contessoto VG, Cheng RR, Oliveira Junior AB, Di Pierro M, Onuchic JN. Structural Reorganization and Relaxation Dynamics of Axially Stressed Chromosomes. Biophysical Journal. PMID 36960531 DOI: 10.1016/j.bpj.2023.03.029  0.701
2023 Contessoto VG, Dudchenko O, Aiden EL, Wolynes PG, Onuchic JN, Di Pierro M. Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. Nature Communications. 14: 326. PMID 36658127 DOI: 10.1038/s41467-023-35909-2  0.427
2023 Bononi A, Wang Q, Zolondick AA, Bai F, Steele-Tanji M, Suarez JS, Pastorino S, Sipes A, Signorato V, Ferro A, Novelli F, Kim JH, Minaai M, Takinishi Y, Pellegrini L, ... ... Onuchic JN, et al. BAP1 is a novel regulator of HIF-1α. Proceedings of the National Academy of Sciences of the United States of America. 120: e2217840120. PMID 36656861 DOI: 10.1073/pnas.2217840120  0.438
2022 Galbraith M, Levine H, Onuchic JN, Jia D. Decoding the coupled decision-making of the epithelial-mesenchymal transition and metabolic reprogramming in cancer. Iscience. 26: 105719. PMID 36582834 DOI: 10.1016/j.isci.2022.105719  0.372
2022 Manna RN, Onuchic JN, Jana B. Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control. Proceedings of the National Academy of Sciences of the United States of America. 120: e2215170120. PMID 36574689 DOI: 10.1073/pnas.2215170120  0.6
2022 Ng Chau K, George JT, Onuchic JN, Lin X, Levine H. Contact map dependence of a T-cell receptor binding repertoire. Physical Review. E. 106: 014406. PMID 35974642 DOI: 10.1103/PhysRevE.106.014406  0.723
2022 Prajapati JD, Onuchic JN, Sanbonmatsu KY. Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts. Journal of Molecular Biology. 167788. PMID 35963460 DOI: 10.1016/j.jmb.2022.167788  0.61
2022 Contessoto VG, Cheng RR, Onuchic JN. Uncovering the statistical physics of 3D chromosomal organization using data-driven modeling. Current Opinion in Structural Biology. 75: 102418. PMID 35839701 DOI: 10.1016/j.sbi.2022.102418  0.709
2022 Freitas FC, Maldonado M, Oliveira Junior AB, Onuchic JN, Oliveira RJ. Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes. The Journal of Chemical Physics. 156: 195101. PMID 35597640 DOI: 10.1063/5.0083875  0.366
2022 Markosian C, Staquicini DI, Dogra P, Dodero-Rojas E, Lubin JH, Tang FHF, Smith TL, Contessoto VG, Libutti SK, Wang Z, Cristini V, Khare SD, Whitford PC, Burley SK, Onuchic JN, et al. Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection. Molecular Biology and Evolution. PMID 35511693 DOI: 10.1093/molbev/msac091  0.581
2022 Vilchez Mercedes SA, Bocci F, Ahmed M, Eder I, Zhu N, Levine H, Onuchic JN, Jolly MK, Wong PK. Nrf2 Modulates the Hybrid Epithelial/Mesenchymal Phenotype and Notch Signaling During Collective Cancer Migration. Frontiers in Molecular Biosciences. 9: 807324. PMID 35480877 DOI: 10.3389/fmolb.2022.807324  0.388
2022 Karmi O, Marjault HB, Bai F, Roy S, Sohn YS, Darash Yahana M, Morcos F, Ioannidis K, Nahmias Y, Jennings PA, Mittler R, Onuchic JN, Nechushtai R. A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35135884 DOI: 10.1073/pnas.2121491119  0.463
2022 Sanches MN, Knapp K, Oliveira AB, Wolynes PG, Onuchic JN, Leite VBP. Examining the Ensembles of Amyloid-β Monomer Variants and Their Propensities to Form Fibers Using an Energy Landscape Visualization Method. The Journal of Physical Chemistry. B. 126: 93-99. PMID 34968059 DOI: 10.1021/acs.jpcb.1c08525  0.427
2021 Lin X, George JT, Schafer NP, Chau KN, Birnbaum ME, Clementi C, Onuchic JN, Levine H. Rapid Assessment of T-Cell Receptor Specificity of the Immune Repertoire. Nature Computational Science. 1: 362-373. PMID 36090450 DOI: 10.1038/s43588-021-00076-1  0.708
2021 Tripathi S, Brahmachari S, Onuchic JN, Levine H. DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases. Nucleic Acids Research. PMID 34951454 DOI: 10.1093/nar/gkab1252  0.392
2021 Novelli F, Bononi A, Wang Q, Bai F, Patergnani S, Kricek F, Haglund E, Suarez JS, Tanji M, Xu R, Takanishi Y, Minaai M, Pastorino S, Morris P, Sakamoto G, ... ... Onuchic JN, et al. BAP1 forms a trimer with HMGB1 and HDAC1 that modulates gene × environment interaction with asbestos. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34815344 DOI: 10.1073/pnas.2111946118  0.458
2021 Markosian C, Staquicini DI, Dogra P, Dodero-Rojas E, Tang FHF, Smith TL, Contessoto VG, Libutti SK, Wang Z, Cristini V, Whitford PC, Burley SK, Onuchic JN, Pasqualini R, Arap W. Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools. Biorxiv : the Preprint Server For Biology. PMID 34676381 DOI: 10.1101/2021.08.30.458222  0.543
2021 de Oliveira AB, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC. SMOG 2 and OpenSMOG: Extending the limits of structure-based models. Protein Science : a Publication of the Protein Society. PMID 34655449 DOI: 10.1002/pro.4209  0.756
2021 Mehrabiani KM, Cheng RR, Onuchic JN. Expanding Direct Coupling Analysis to Identify Heterodimeric Interfaces from Limited Protein Sequence Data. The Journal of Physical Chemistry. B. PMID 34618469 DOI: 10.1021/acs.jpcb.1c07145  0.798
2021 Dodero-Rojas E, Onuchic JN, Whitford PC. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. Elife. 10. PMID 34463614 DOI: 10.7554/eLife.70362  0.634
2021 Vilchez Mercedes SA, Bocci F, Levine H, Onuchic JN, Jolly MK, Wong PK. Decoding leader cells in collective cancer invasion. Nature Reviews. Cancer. PMID 34239104 DOI: 10.1038/s41568-021-00376-8  0.383
2021 Staquicini DI, Tang FHF, Markosian C, Yao VJ, Staquicini FI, Dodero-Rojas E, Contessoto VG, Davis D, O'Brien P, Habib N, Smith TL, Bruiners N, Sidman RL, Gennaro ML, Lattime EC, ... ... Onuchic JN, et al. Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34234013 DOI: 10.1073/pnas.2105739118  0.557
2021 Sarkar R, Jaiswar A, Hennelly SP, Onuchic JN, Sanbonmatsu KY, Roy S. Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation. The Journal of Physical Chemistry. B. PMID 34106719 DOI: 10.1021/acs.jpcb.1c02467  0.574
2021 Oliveira Junior AB, Lin X, Kulkarni P, Onuchic JN, Roy S, Leite VBP. Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms. Journal of Chemical Theory and Computation. PMID 33871257 DOI: 10.1021/acs.jctc.1c00027  0.723
2021 Jia D, Park JH, Kaur H, Jung KH, Yang S, Tripathi S, Galbraith M, Deng Y, Jolly MK, Kaipparettu BA, Onuchic JN, Levine H. Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer. British Journal of Cancer. PMID 33859341 DOI: 10.1038/s41416-021-01385-y  0.372
2021 Staquicini DI, Tang FHF, Markosian C, Yao VJ, Staquicini FI, Dodero-Rojas E, Contessoto VG, Davis D, O'Brien P, Habib N, Smith TL, Bruiners N, Sidman RL, Gennaro ML, Lattime EC, ... ... Onuchic JN, et al. Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain. Biorxiv : the Preprint Server For Biology. PMID 33758865 DOI: 10.1101/2021.03.15.435496  0.561
2021 Dutta M, Gilbert SP, Onuchic JN, Jana B. Mechanistic basis of propofol-induced disruption of kinesin processivity. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33495322 DOI: 10.1073/pnas.2023659118  0.609
2020 Kohar V, Gordin D, Katebi A, Levine H, Onuchic JN, Lu M. Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. Bioinformatics (Oxford, England). PMID 33279968 DOI: 10.1093/bioinformatics/btaa785  0.391
2020 Cheng RR, Contessoto V, Lieberman-Aiden E, Wolynes PG, Di Pierro M, Onuchic JN. Exploring chromosomal structural heterogeneity across multiple cell lines. Elife. 9. PMID 33047670 DOI: 10.7554/eLife.60312  0.769
2020 Contessoto VG, Cheng RR, Hajitaheri A, Dodero-Rojas E, Mello MF, Lieberman-Aiden E, Wolynes PG, Di Pierro M, Onuchic JN. The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. Nucleic Acids Research. PMID 33021634 DOI: 10.1093/nar/gkaa818  0.746
2020 Jia D, Paudel BB, Hayford CE, Hardeman KN, Levine H, Onuchic JN, Quaranta V. Drug-Tolerant Idling Melanoma Cells Exhibit Theory-Predicted Metabolic Low-Low Phenotype. Frontiers in Oncology. 10: 1426. PMID 32923395 DOI: 10.3389/Fonc.2020.01426  0.433
2020 Guo WH, Qi X, Yu X, Liu Y, Chung CI, Bai F, Lin X, Lu D, Wang L, Chen J, Su LH, Nomie KJ, Li F, Wang MC, Shu X, ... Onuchic JN, et al. Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry. Nature Communications. 11: 4268. PMID 32848159 DOI: 10.1038/S41467-020-17997-6  0.75
2020 Huang B, Lu M, Galbraith M, Levine H, Onuchic JN, Jia D. Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation. Journal of the Royal Society, Interface. 17: 20200500. PMID 32781932 DOI: 10.1098/Rsif.2020.0500  0.451
2020 Jin S, Chen M, Chen X, Bueno C, Lu W, Schafer NP, Lin X, Onuchic JN, Wolynes PG. Protein Structure Prediction in CASP13 using AWSEM-Suite. Journal of Chemical Theory and Computation. PMID 32396727 DOI: 10.1021/Acs.Jctc.0C00188  0.773
2020 Danielsson J, Noel JK, Simien JM, Duggan BM, Oliveberg M, Onuchic JN, Jennings PA, Haglund E. The Pierced Lasso Topology Leptin has a Bolt on Dynamic Domain Composed by the Disordered Loops I and III. Journal of Molecular Biology. PMID 32081588 DOI: 10.1016/J.Jmb.2020.01.035  0.688
2020 Shibata M, Lin X, Cheng RR, Yura K, Onuchic JN. Comparative Analysis of the Residue Co-Evolution of the DNA-Binding Response Regulator Subfamilies Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.1439  0.681
2019 Krepel D, Davtyan A, Schafer NP, Wolynes PG, Onuchic JN. Braiding topology and the energy landscape of chromosome organization proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 31888987 DOI: 10.1073/Pnas.1917750117  0.564
2019 Kang TY, Bocci F, Jolly MK, Levine H, Onuchic JN, Levchenko A. Pericytes enable effective angiogenesis in the presence of proinflammatory signals. Proceedings of the National Academy of Sciences of the United States of America. PMID 31685607 DOI: 10.1073/Pnas.1913373116  0.449
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  0.534
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  0.441
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  0.45
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  0.385
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  0.778
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  0.794
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  0.522
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  0.439
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  0.755
2019 Bocci F, Jolly MK, Levine H, Onuchic JN. Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks. Methods in Molecular Biology (Clifton, N.J.). 1912: 341-366. PMID 30635901 DOI: 10.1007/978-1-4939-8982-9_14  0.518
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  0.609
2019 Bocci F, Gearhart-Serna L, Boareto M, Ribeiro M, Ben-Jacob E, Devi GR, Levine H, Onuchic JN, Jolly MK. Toward understanding cancer stem cell heterogeneity in the tumor microenvironment. Proceedings of the National Academy of Sciences of the United States of America. 116: 148-157. PMID 30587589 DOI: 10.1073/Pnas.1815345116  0.456
2019 Wang J, Onuchic J, Wolynes P. Statistics of kinetic pathways on biased rough energy landscapes with applications to protein folding. Physical Review Letters. 76: 4861-4864. PMID 10061399 DOI: 10.1103/Physrevlett.76.4861  0.553
2019 Jia D, Lu M, Jung KH, Park JH, Onuchic JN, Kaipparettu BA, Levine H. Abstract 2448: Elucidating the metabolic plasticity of cancer by coupling gene regulation with metabolic pathways Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-2448  0.411
2019 Bocci F, Levine H, Onuchic JN, Jolly MK. Deciphering the Dynamics of Epithelial-Mesenchymal Transition and Cancer Stem Cells in Tumor Progression Stem Cell Reports. 5: 11-21. DOI: 10.1007/S40778-019-0150-3  0.307
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  0.437
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  0.768
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  0.636
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  0.673
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  0.782
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  0.731
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  0.773
2018 Bocci F, Jolly MK, George JT, Levine H, Onuchic JN. A mechanism-based computational model to capture the interconnections among epithelial-mesenchymal transition, cancer stem cells and Notch-Jagged signaling. Oncotarget. 9: 29906-29920. PMID 30042822 DOI: 10.18632/Oncotarget.25692  0.463
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  0.802
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  0.511
2018 Haglund E, Nguyen L, Schafer NP, Lammert H, Jennings PA, Onuchic JN. Uncovering the molecular mechanisms behind disease-associated leptin variants. The Journal of Biological Chemistry. PMID 29950524 DOI: 10.1074/Jbc.Ra118.003957  0.304
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  0.444
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  0.769
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  0.512
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  0.73
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  0.41
2018 Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Padilla PA, Azad RK, Mittler R. Phylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin. Scientific Reports. 8: 4840. PMID 29556009 DOI: 10.1038/S41598-018-23305-6  0.336
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  0.509
2018 Karmi O, Marjault HB, Pesce L, Carloni P, Onuchic JN, Jennings PA, Mittler R, Nechushtai R. The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. PMID 29435647 DOI: 10.1007/S00775-018-1538-8  0.339
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  0.323
2018 Onuchic JN, Morcos F. Protein Sequence Coevolution, Energy Landscapes and their Connections to Protein Structure, Folding and Function Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.2151  0.422
2018 Lin X, Noel JK, Wang Q, Ma J, Onuchic JN. Atomistic Simulations Reveal a Hindered Transition of the B-Loop Domain of Influenza Hemagglutinin Biophysical Journal. 114: 232a. DOI: 10.1016/J.Bpj.2017.11.1292  0.777
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  0.368
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  0.348
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  0.462
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: 10.1016/J.Bpj.2017.11.3265  0.764
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  0.693
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  0.716
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  0.641
2017 Karmi O, Holt SH, Song L, Tamir S, Luo Y, Bai F, Adenwalla A, Darash-Yahana M, Sohn YS, Jennings PA, Azad RK, Onuchic JN, Morcos F, Nechushtai R, Mittler R. Interactions between mitoNEET and NAF-1 in cells. Plos One. 12: e0175796. PMID 28426722 DOI: 10.1371/Journal.Pone.0175796  0.518
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  0.477
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  0.622
2017 Inupakutika MA, Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Azad RK, Padilla P, Mittler R. Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates. Scientific Reports. 7: 42571. PMID 28205535 DOI: 10.1038/Srep42571  0.367
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  0.45
2017 Wang Q, Cheung M, Diehl M, Onuchic J, Jana B, Kolomeisky A. Cooperativity of Kinesin Motor Proteins under External Loads Biophysical Journal. 112: 426a. DOI: 10.1016/J.Bpj.2016.11.2277  0.704
2016 Haglund E, Pilko A, Wollman R, Jennings PA, Onuchic JN. The Pierced Lasso Topology Controls Function in Leptin. The Journal of Physical Chemistry. B. PMID 28035835 DOI: 10.1021/Acs.Jpcb.6B11506  0.373
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  0.798
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  0.784
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  0.527
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  0.511
2016 Cheng RR, Nordesjö O, Hayes RL, Levine H, Flores SC, Onuchic JN, Morcos F. Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes. Molecular Biology and Evolution. PMID 27604223 DOI: 10.1093/Molbev/Msw188  0.35
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  0.799
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  0.63
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  0.542
2016 Boareto M, Jolly MK, Goldman A, Pietilä M, Mani SA, Sengupta S, Ben-Jacob E, Levine H, Onuchic JN. Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype. Journal of the Royal Society, Interface / the Royal Society. 13. PMID 27170649 DOI: 10.1098/Rsif.2015.1106  0.451
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  0.773
2016 Phillips GN, Onuchic JN. Preface to Special Topic on Protein Dynamics: Beyond Static Snapshots in Structural Biology. Structural Dynamics (Melville, N.Y.). 3: 011901. PMID 27042685 DOI: 10.1063/1.4942424  0.35
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  0.784
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  0.715
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  0.374
2016 Lin X, Noel JK, Eddy NR, Ma J, Onuchic JN. Investigation of the pH Induced Conformational Rearrangement of Influenza Hemagglutinin Biophysical Journal. 110: 13a. DOI: 10.1016/J.Bpj.2015.11.126  0.792
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  0.725
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  0.681
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  0.662
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  0.447
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  0.819
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  0.783
2015 Onuchic JN. 47 The energy landscape for protein folding and biomolecular machines. Journal of Biomolecular Structure & Dynamics. 33: 33. PMID 26103259 DOI: 10.1080/07391102.2015.1032596  0.352
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  0.513
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  0.628
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  0.679
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  0.362
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  0.33
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  0.766
2015 Hayes RL, Noel JK, Mandic A, Whitford PC, Sanbonmatsu KY, Mohanty U, Onuchic JN. Magnesium Dependence of the RNA Free Energy Landscape Biophysical Journal. 108: 235a. DOI: 10.1016/J.Bpj.2014.11.1301  0.797
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  0.706
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  0.795
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  0.448
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  0.802
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  0.714
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  0.387
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  0.788
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  0.708
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  0.387
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  0.774
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  0.425
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  0.708
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  0.443
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  0.356
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  0.404
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  0.703
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  0.553
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  0.361
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  0.663
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  0.744
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  0.723
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  0.377
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  0.625
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  0.819
2012 Beratan DN, Onuchic JN. Redox redux. Physical Chemistry Chemical Physics : Pccp. 14: 13728. PMID 22960628 DOI: 10.1039/c2cp90148j  0.403
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  0.718
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  0.758
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  0.401
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  0.373
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  0.399
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  0.78
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  0.766
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  0.71
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  0.307
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  0.423
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  0.686
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  0.579
2012 Hayes RL, Onuchic J, Noel J, Sanbonmatsu K, Mohanty U. Glass-Like Behavior of Magnesium Ions Inside RNA APTamers Biophysical Journal. 102: 646a. DOI: 10.1016/J.Bpj.2011.11.3519  0.607
2012 Sun L, Sulkowska J, Noel J, Onuchic J. The Force-Induced Activation of Talin in a Structure-Based Model Simulation Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.311  0.694
2012 Noel J, Sulkowska J, Onuchic J. Protein Knot Forming, Terminal-Through-Loop Threading Events can Occur on the Microsecond (<10) Timescale Biophysical Journal. 102: 458a. DOI: 10.1016/J.Bpj.2011.11.2515  0.727
2012 Haglund E, Sulkowska JI, Jennings PA, Onuchic J. Structure Based Protein Models and In Vitro Experiments to Investigate the Folding Landscape of the Human Obesity Protein Leptin Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.2514  0.39
2012 Lammert H, Noel JK, Onuchic JN. The Geometrical Origins of a Protein Folding Mechanism Biophysical Journal. 102: 448a. DOI: 10.1016/J.Bpj.2011.11.2457  0.72
2012 Jana B, Hyeon C, Onuchic JN. Exploring the Origin of Directionality of Ncd Motor using Structure-Based Model Biophysical Journal. 102: 371a. DOI: 10.1016/J.Bpj.2011.11.2028  0.749
2012 Morcos F, Pagnini A, Lunt B, Bertolino A, Marks D, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Estimation of Residue-Residue Coevolution using Direct Coupling Analysis Identifies Many Native Contacts Across a Large Number of Domain Families Biophysical Journal. 102: 250a. DOI: 10.1016/J.Bpj.2011.11.1378  0.404
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  0.599
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  0.425
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  0.761
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  0.726
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  0.357
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  0.356
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  0.671
2011 Whitford PC, Spahn CM, Blanchard SC, Onuchic JN, Sanbonmatsu KY. Revealing the Energy Landscapes of Ribosome Function Biophysical Journal. 100: 238a. DOI: 10.1016/J.Bpj.2010.12.1517  0.762
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  0.732
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  0.452
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  0.359
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  0.736
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  0.661
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  0.734
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  0.808
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  0.819
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  0.771
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  0.45
2010 Suzuki Y, Noel J, Onuchic J. 2P063 Analytical Model for Protein Folding improved by introducting topological factors(The 48th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 50. DOI: 10.2142/Biophys.50.S93_1  0.648
2010 Lammert H, Onuchic JN. The Mechanism of Geometrical Frustration in SH3 Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.3497  0.445
2010 Whitford PC, Geggier P, Altman R, Blanchard SC, Onuchic JN, Sanbonmatsu KY. Simulations of the Ribosome Suggest Reversible Transitions and Parallel Pathways are Involved in the Large-Scale Functional Motions of tRNA During Translation Biophysical Journal. 98: 259a. DOI: 10.1016/J.Bpj.2009.12.1412  0.653
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: 10.1016/J.Bpj.2009.12.1285  0.411
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  0.412
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  0.5
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  0.376
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  0.48
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  0.563
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  0.445
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  0.455
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  0.63
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  0.744
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  0.821
2009 Schug A, Gambin Y, Deniz A, Onuchic J. The Rop-Dimer: A Folded Protein Living Between Two Alternate Structures Biophysical Journal. 96: 568a. DOI: 10.1016/J.Bpj.2008.12.3722  0.42
2009 Whitford PC, Schug A, Noel JK, Gosavi S, Hennelly SP, Sanbonmatsu KY, Onuchic JN. All-atom Models For RNA And Proteins: Simulating Folding And Function Biophysical Journal. 96: 555a. DOI: 10.1016/J.Bpj.2008.12.3648  0.823
2009 Gosavi S, Andrews B, Jennings P, Onuchic J. Multilevel Modeling To Understand The Folding Hysteresis Of GFP Biophysical Journal. 96: 330a. DOI: 10.1016/J.Bpj.2008.12.1661  0.388
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  0.717
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  0.512
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  0.311
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  0.427
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  0.584
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  0.423
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  0.704
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  0.645
2008 Onuchic JN. Special issue on protein folding: Experimental and theoretical approaches Hfsp Journal. 2: 295-296. DOI: 10.2976/1.3023645  0.471
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. DOI: 10.1590/S0103-50532008000200003  0.377
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  0.684
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  0.666
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  0.516
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  0.585
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  0.747
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  0.505
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  0.576
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  0.548
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  0.685
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  0.606
2007 Suzuki Y, Onuchic JN. 2P114 Analytical Model for Protein Folding(Proteins-stability, folding, and other physicochemical properties,Poster Presentations) Seibutsu Butsuri. 47. DOI: 10.2142/Biophys.47.S141_3  0.392
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  0.432
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  0.76
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  0.596
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  0.403
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  0.72
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  0.34
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  0.718
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  0.436
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  0.577
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  0.489
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  0.48
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  0.753
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  0.54
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  0.761
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  0.395
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  0.36
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  0.711
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  0.338
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  0.691
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  0.586
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  0.347
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  0.386
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  0.809
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  0.608
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+  0.758
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  0.606
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  0.55
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  0.608
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  0.41
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  0.64
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  0.575
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  0.586
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  0.798
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  0.436
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  0.54
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  0.385
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  0.439
2003 Kobayashi C, Baldridge K, Onuchic J. A theoretical study of Electron transfer in protein : Influence of protein dynamics and hydrogen bonds Seibutsu Butsuri. 43. DOI: 10.2142/Biophys.43.S26_4  0.33
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  0.569
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  0.33
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. DOI: 10.1021/Jp034441R  0.642
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  0.36
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  0.325
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  0.749
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  0.699
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  0.714
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 DOI: 10.1103/Physrevlett.88.168101  0.804
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  0.642
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  0.31
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  0.47
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  0.444
2001 Brooks CL, Onuchic JN, Wales DJ. Statistical thermodynamics: Taking a walk on a landscape Science. 293: 612-613. PMID 11474087 DOI: 10.1126/Science.1062559  0.484
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  0.313
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  0.344
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  0.439
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  0.405
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  0.769
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  0.761
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  0.756
2000 García AE, Hillson N, Onuchic JN. Solvent effects on protein folding/unfolding Progress of Theoretical Physics Supplement. 282-291. DOI: 10.1143/Ptps.138.282  0.368
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  0.667
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  0.304
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  0.668
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  0.353
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  0.577
1999 Onuchic JN, Wang J, Wolynes PG. Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions Chemical Physics. 247: 175-184. DOI: 10.1016/S0301-0104(99)00203-7  0.512
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  0.586
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  0.358
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  0.577
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  0.753
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. DOI: 10.1063/1.475828  0.398
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. DOI: 10.1021/Jp9819442  0.338
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  0.601
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  0.44
1997 Socci ND, Nymeyer H, Onuchic JN. Exploring the protein folding funnel landscape Physica D: Nonlinear Phenomena. 107: 366-382. DOI: 10.1016/S0167-2789(97)00105-X  0.745
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 DOI: 10.1021/Cr9500444  0.481
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  0.575
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 DOI: 10.1016/S1074-5521(96)90090-3  0.579
1996 Socci ND, Onuchic JN, Wolynes PG. Diffusive dynamics of the reaction coordinate for protein folding funnels The Journal of Chemical Physics. 104: 5860-5868. DOI: 10.1063/1.471317  0.548
1996 Leite VBP, Onuchic JN. Structure and Dynamics of Solvent Landscapes in Charge-Transfer Reactions The Journal of Physical Chemistry. 100: 7680-7690. DOI: 10.1021/Jp951316+  0.32
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.  0.479
1995 Curry WB, Grabe MD, Kurnikov IV, Skourtis SS, Beratan DN, Regan JJ, Aquino AJ, Beroza P, Onuchic JN. Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins. Journal of Bioenergetics and Biomembranes. 27: 285-93. PMID 8847342 DOI: 10.1007/Bf02110098  0.582
1995 Wolynes PG, Onuchic JN, Thirumalai D. Navigating the folding routes. Science (New York, N.Y.). 267: 1619-20. PMID 7886447 DOI: 10.1126/Science.7886447  0.485
1995 Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 21: 167-95. PMID 7784423 DOI: 10.1002/Prot.340210302  0.612
1995 Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND. Toward an outline of the topography of a realistic protein-folding funnel. Proceedings of the National Academy of Sciences of the United States of America. 92: 3626-30. PMID 7724609 DOI: 10.1073/Pnas.92.8.3626  0.61
1995 Socci ND, Onuchic JN. Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique Journal of Chemical Physics. 103: 4732-4744. DOI: 10.1063/1.470610  0.363
1995 Betancourt MR, Onuchic JN. Kinetics Of Proteinlike Models : The Energy Landscape Factors That Determine Folding Journal of Chemical Physics. 103: 773-787. DOI: 10.1063/1.470109  0.77
1994 Socci ND, Bialek WS, Onuchic JN. Properties and origins of protein secondary structure. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 49: 3440-3443. PMID 9961612 DOI: 10.1103/Physreve.49.3440  0.452
1994 Socci ND, Onuchic JN. Folding kinetics of proteinlike heteropolymers Journal of Chemical Physics. 101: 1519-1528. DOI: 10.1063/1.467775  0.347
1993 Onuchic JN, Wolynes PG. Energy landscapes, glass transitions, and chemical reaction dynamics in biomolecular or solvent environment The Journal of Chemical Physics. 98: 2218-2224. DOI: 10.1063/1.464201  0.502
1993 Regan JJ, Risser SM, Beratan DN, Onuchic JN. Protein electron transport: Single versus multiple pathways Journal of Physical Chemistry. 97: 13083-13088. DOI: 10.1021/J100152A009  0.56
1993 Risser SM, Beratan DN, Onuchic JN. Electronic coupling in starburst dendrimers: Connectivity, disorder, and finite size effects in macromolecular Bethe lattices Journal of Physical Chemistry. 97: 4523-4527. DOI: 10.1021/J100119A045  0.51
1992 Leopold PE, Montal M, Onuchic JN. Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proceedings of the National Academy of Sciences of the United States of America. 89: 8721-5. PMID 1528885 DOI: 10.1073/Pnas.89.18.8721  0.64
1992 Beratan DN, Onuchic JN, Winkler JR, Gray HB. Electron-tunneling pathways in proteins. Science (New York, N.Y.). 258: 1740-1. PMID 1334572 DOI: 10.1126/Science.1334572  0.527
1992 Onuchic JN, Beratan DN, Winkler JR, Gray HB. Pathway analysis of protein electron-transfer reactions. Annual Review of Biophysics and Biomolecular Structure. 21: 349-77. PMID 1326356 DOI: 10.1146/Annurev.Bb.21.060192.002025  0.611
1992 Betts JN, Beratan DN, Onuchic JN. Mapping electron tunneling pathways: An algorithm that finds the "minimum lengths"/maximum coupling pathway between electron donors and acceptors in proteins Journal of the American Chemical Society. 114: 4043-4046. DOI: 10.1021/Ja00037A004  0.529
1992 Beratan DN, Betts JN, Onuchic JN. Tunneling pathway and redox-state-dependent electronic couplings at nearly fixed distance in electron-transfer proteins Journal of Physical Chemistry. 96: 2852-2855. DOI: 10.1021/J100186A014  0.558
1991 Beratan DN, Betts JN, Onuchic JN. Protein electron transfer rates set by the bridging secondary and tertiary structure. Science (New York, N.Y.). 252: 1285-8. PMID 1656523 DOI: 10.1126/Science.1656523  0.579
1991 Onuchic JN, De Andrade PCP, Beratan DN. Electron tunneling pathways in proteins: A method to compute tunneling matrix elements in very large systems The Journal of Chemical Physics. 95: 1131-1138. DOI: 10.1063/1.461142  0.527
1990 Onuchic JN, Beratan DN. A predictive theoretical model for electron tunneling pathways in proteins The Journal of Chemical Physics. 92: 722-733. DOI: 10.1063/1.458426  0.567
1990 Beratan DN, Onuchic JN, Betts JN, Bowler BE, Gray HB. Electron tunneling pathways in ruthenated proteins Journal of the American Chemical Society. 112: 7915-7921. DOI: 10.1021/Ja00178A011  0.552
1989 Beratan DN, Onuchic JN. Electron tunneling pathways in proteins: influences on the transfer rate. Photosynthesis Research. 22: 173-86. PMID 24424807 DOI: 10.1007/Bf00048296  0.556
1989 Bialek W, Bruno WJ, Joseph J, Onuchic JN. Quantum and classical dynamics in biochemical reactions. Photosynthesis Research. 22: 15-27. PMID 24424675 DOI: 10.1007/Bf00114763  0.329
1989 Hopfield JJ, Onuchic JN, Beratan DN. Electronic shift register memory based on molecular electron-transfer reactions Journal of Physical Chemistry. 93: 6350-6357. DOI: 10.1021/J100354A017  0.638
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  0.602
1988 Cowan JA, Upmacis RK, Beratan DN, Onuchic JN, Gray HB. Long-range electron transfer in myoglobin. Annals of the New York Academy of Sciences. 550: 68-84. PMID 3245652 DOI: 10.1111/J.1749-6632.1988.Tb35324.X  0.53
1988 Beratan DN, Onuchic JN. Adiabaticlty and nonadiabaticity in bimolecular outer-sphere charge transfer reactions The Journal of Chemical Physics. 89: 6195-6203. DOI: 10.1063/1.455436  0.521
1988 Onuchic JN, Wolynes PG. Classical and quantum pictures of reaction dynamics in condensed matter: resonances, dephasing, and all that The Journal of Physical Chemistry. 92: 6495-6503. DOI: 10.1021/J100334A007  0.47
1988 Onuchic JN, Beratan DN. Adiabaticity criteria for outer-sphere bimolecular electron-transfer reactions Journal of Physical Chemistry. 92: 4817-4820. DOI: 10.1021/J100328A001  0.528
1987 Beratan DN, Onuchic JN, Hopfield JJ. Electron tunneling through covalent and noncovalent pathways in proteins The Journal of Chemical Physics. 86: 4488-4498. DOI: 10.1063/1.452723  0.669
1987 Onuchic JN, Beratan DN. Molecular bridge effects on distant charge tunneling Journal of the American Chemical Society. 109: 6771-6778. DOI: 10.1021/Ja00256A035  0.511
1987 Beratan DN, Onuchic JN, Perry JW. Nonlinear susceptibilities of finite conjugated organic polymers Journal of Physical Chemistry. 91: 2696-2698. DOI: 10.1021/J100295A009  0.502
1986 Onuchic JN, Beratan DN, Hopfield JJ. Some aspects of electron-transfer reaction dynamics Journal of Physical Chemistry. 90: 3707-3721. DOI: 10.1021/J100407A045  0.629
1985 Beratan DN, Onuchic JN, Hopfield JJ. Limiting forms of the tunneling matrix element in the long distance bridge mediated electron transfer problem The Journal of Chemical Physics. 83: 5325-5329. DOI: 10.1063/1.449694  0.642
Low-probability matches (unlikely to be authored by this person)
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  0.299
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  0.296
1994 Skourtis SS, Regan JJ, Onuchic JN. Electron transfer in proteins: a novel approach for the description of donor-acceptor coupling The Journal of Physical Chemistry. 98: 3379-3388. DOI: 10.1021/J100064A019  0.296
1996 Balabin IA, Onuchic JN. Connection between Simple Models and Quantum Chemical Models for Electron-Transfer Tunneling Matrix Element Calculations: A Dyson's Equations-Based Approach The Journal of Physical Chemistry. 100: 11573-11580. DOI: 10.1021/Jp953568G  0.295
2014 Huang B, Lu M, Jolly MK, Onuchic J, Ben-Jacob E. Multistability in GTPase-Based Decision Circuits Biophysical Journal. 106: 379a-380a. DOI: 10.1016/J.Bpj.2013.11.2147  0.294
2016 Lu M, Capello M, Tripathi SC, Levine H, Ben-Jacob E, Hanash SM, Onuchic J. Abstract 779: The role of exosome-mediated cell-cell communication in inducing phenotypic changes Cancer Research. 76: 779-779. DOI: 10.1158/1538-7445.Am2016-779  0.291
1995 Regan JJ, Di Bilio AJ, Langen R, Skov LK, Winkler JR, Gray HB, Onuchic JN. Electron tunneling in azurin: the coupling across a beta-sheet. Chemistry & Biology. 2: 489-96. PMID 9383451 DOI: 10.1016/1074-5521(95)90266-X  0.289
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  0.288
1993 Skourtis SS, Onuchic JN. Effective two-state systems in bridge-mediated electron transfer. A Green function analysis Chemical Physics Letters. 209: 171-177. DOI: 10.1016/0009-2614(93)87219-S  0.287
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  0.284
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  0.284
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  0.283
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  0.282
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  0.282
1986 Onuchic JN, Gama AASd. Influence of intersite modes on the exchange interaction in electron transfer at large distances Theoretical Chemistry Accounts. 69: 89-100. DOI: 10.1007/Bf00527681  0.282
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  0.281
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  0.28
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  0.28
1987 Onuchic JN. Effect of friction on electron transfer: The two reaction coordinate case Journal of Chemical Physics. 86: 3925-3943. DOI: 10.1063/1.451952  0.278
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  0.277
2014 Lu M, Onuchic J, Ben-Jacob E. Construction of a Self-Consistent Landscape for Multistable Gene Regulatory Circuits Biophysical Journal. 106: 379a. DOI: 10.1016/J.Bpj.2013.11.2146  0.274
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  0.274
1992 Skourtis SS, Da Silva AJR, Bialek W, Onuchic JN. A new look at the primary charge separation in bacterial photosynthesis Journal of Physical Chemistry. 96: 8034-8041. DOI: 10.1021/J100199A038  0.272
1988 Onuchic JN, Corongiu G. Determination of the water geometry in violuric acid monohydrate with a Monte Carlo simulation Journal of Computational Chemistry. 9: 11-17. DOI: 10.1002/Jcc.540090103  0.272
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  0.27
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  0.268
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  0.267
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  0.267
2020 Bocci F, Onuchic JN, Jolly MK. Understanding the Principles of Pattern Formation Driven by Notch Signaling by Integrating Experiments and Theoretical Models. Frontiers in Physiology. 11: 929. PMID 32848867 DOI: 10.3389/Fphys.2020.00929  0.265
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  0.264
2019 Bocci F, Jolly MK, Onuchic JN. A Biophysical Model Uncovers the Size Distribution of Migrating Cell Clusters across Cancer Types. Cancer Research. 79: 5527-5535. PMID 31481500 DOI: 10.1158/0008-5472.Can-19-1726  0.264
2018 Jolly MK, Bocci F, Tripathi SC, Aguilar M, Hanash SM, Levine H, Onuchic JN. Abstract 4999: Identifying intercellular phenotypic stability factors for a hybrid epithelial-mesenchymal phenotype Cancer Research. 78: 4999-4999. DOI: 10.1158/1538-7445.Am2018-4999  0.261
1985 Garg A, Onuchic JN, Ambegaokar V. Effect of friction on electron transfer in biomolecules Journal of Chemical Physics. 83: 4491-4503. DOI: 10.1063/1.449017  0.261
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  0.256
2015 Lu M, Jolly MK, Hannash SM, Levine H, Onuchic JN, Ben-Jacob E. Modeling Epithelial-Mesenchymal Transitions in Metastatic Cancer Biophysical Journal. 108: 313a. DOI: 10.1016/J.Bpj.2014.11.1701  0.255
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  0.252
2020 Dodero-Rojas E, Ferreira LG, Leite VBP, Onuchic JN, Contessoto VG. Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro. Plos One. 15: e0222900. PMID 31990920 DOI: 10.1371/Journal.Pone.0222900  0.251
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  0.25
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  0.249
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  0.249
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  0.248
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  0.246
2022 Magi Meconi G, Sasselli I, Bianco V, Onuchic J, Coluzza I. Key aspects of the past 30 Years of protein design. Reports On Progress in Physics. Physical Society (Great Britain). PMID 35704983 DOI: 10.1088/1361-6633/ac78ef  0.245
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  0.241
2018 Carbone M, Amelio I, Affar EB, Brugarolas J, Cannon-Albright LA, Cantley LC, Cavenee WK, Chen Z, Croce CM, Andrea A, Gandara D, Giorgi C, Jia W, Lan Q, Mak TW, ... ... Onuchic JN, et al. Consensus report of the 8 and 9th Weinman Symposia on Gene x Environment Interaction in carcinogenesis: novel opportunities for precision medicine. Cell Death and Differentiation. PMID 30323273 DOI: 10.1038/S41418-018-0213-5  0.241
2017 Jia D, Yu L, Lu M, Ben-Jacob E, Ma J, Levine H, Kaipparettu BA, Onuchic J. Abstract 5568: Towards decoding the interplay between glycolysis and oxidative phosphorylation in cancer Cancer Research. 77: 5568-5568. DOI: 10.1158/1538-7445.Am2017-5568  0.239
2012 Stavropoulos T, Schultz D, Onuchic JN, Jacob EB. Breaking the Code of Bacteria Decision Making Biophysical Journal. 102: 2-8. DOI: 10.1016/J.Bpj.2011.11.1593  0.237
2014 Jolly MK, Lu M, Levine H, Onuchic JN, Ben-Jacob E. Abstract 1133: Partial EMT, hybrid epithelial-mesenchymal phenotype and epithelial plasticity: role of (miR-200/ZEB) loop Cancer Research. 74: 1133-1133. DOI: 10.1158/1538-7445.Am2014-1133  0.234
2022 Freitas FC, Maldonado M, Oliveira Junior AB, Onuchic JN, Oliveira RJ. Erratum: "Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes" [J. Chem. Phys. 156, 195101 (2022)]. The Journal of Chemical Physics. 157: 049901. PMID 35922346 DOI: 10.1063/5.0105358  0.234
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  0.233
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  0.229
2014 Onuchic JN. Physics transforming the life sciences. Physical Biology. 11: 053006. PMID 25293472 DOI: 10.1088/1478-3975/11/5/053006  0.222
1997 Pande VS, Onuchic JN. Electron Transport in Disordered Polymeric and Biological Systems Physical Review Letters. 78: 146-149. DOI: 10.1103/Physrevlett.78.146  0.208
1997 Nelson ED, Teneyck LF, Onuchic JN. Symmetry and kinetic optimization of proteinlike heteropolymers Physical Review Letters. 79: 3534-3537. DOI: 10.1103/Physrevlett.79.3534  0.208
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  0.206
2024 Shibata M, Lin X, Onuchic JN, Yura K, Cheng RR. Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies. Biophysical Journal. PMID 38291753 DOI: 10.1016/j.bpj.2024.01.028  0.206
1996 Socci ND, Onuchic JN, Wolynes PG. Diffusive dynamics of the reaction coordinate for protein folding funnels Journal of Chemical Physics. 104: 5860-5868.  0.201
2023 Lu W, Onuchic JN, Di Pierro M. An associative memory Hamiltonian model for DNA and nucleosomes. Plos Computational Biology. 19: e1011013. PMID 36972316 DOI: 10.1371/journal.pcbi.1011013  0.2
2023 Dodero-Rojas E, Mello MF, Brahmachari S, Oliveira Junior AB, Contessoto VG, Onuchic JN. PyMEGABASE: Predicting Cell-Type-Specific Structural Annotations of Chromosomes Using the Epigenome. Journal of Molecular Biology. 435: 168180. PMID 37302549 DOI: 10.1016/j.jmb.2023.168180  0.198
1999 Regan JJ, Onuchic JN. Electron-transfer tubes Advances in Chemical Physics. 107: 497-553. DOI: 10.1002/9780470141663.Ch9  0.197
2021 Ngo K, Bruno da Silva F, Leite VBP, Contessoto VG, Onuchic JN. Improving the Thermostability of Xylanase A from by Combining Bioinformatics and Electrostatic Interactions Optimization. The Journal of Physical Chemistry. B. PMID 33887137 DOI: 10.1021/acs.jpcb.1c01253  0.196
2020 Oliveira Junior AB, Contessoto VG, Mello MF, Onuchic JN. A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes. Journal of Molecular Biology. PMID 33160979 DOI: 10.1016/j.jmb.2020.10.034  0.191
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  0.18
2003 Sung NS, Gordon JI, Rose GD, Getzoff ED, Kron SJ, Mumford D, Onuchic JN, Scherer NF, Sumners DL, Kopell NJ. Science education. Educating future scientists. Science (New York, N.Y.). 301: 1485. PMID 12970550 DOI: 10.1126/Science.1086133  0.172
2020 Onuchic JN, Rubtsov IV, Therien MJ. Tribute to David N. Beratan. The Journal of Physical Chemistry. B. 124: 3437-3440. PMID 32349485 DOI: 10.1021/Acs.Jpcb.0C02606  0.17
2021 Oliveira Junior AB, Estrada CP, Aiden EL, Contessoto VG, Onuchic JN. Chromosome Modeling on Downsampled Hi-C Maps Enhances the Compartmentalization Signal. The Journal of Physical Chemistry. B. 125: 8757-8767. PMID 34319725 DOI: 10.1021/acs.jpcb.1c04174  0.165
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.  0.162
1998 Regan JJ, Chang FK, Onuchic JN. Tubular breakdown of electron transfer in proteins Advances in Chemistry Series. 254: 111-129.  0.16
2023 Bocci F, Jia D, Nie Q, Jolly MK, Onuchic J. Theoretical and computational tools to model multistable gene regulatory networks. Reports On Progress in Physics. Physical Society (Great Britain). 86. PMID 37531952 DOI: 10.1088/1361-6633/acec88  0.155
2023 Bocci F, Jia D, Nie Q, Jolly MK, Onuchic J. Theoretical and computational tools to model multistable gene regulatory networks. Arxiv. PMID 36824430  0.155
2022 Brahmachari S, Contessoto VG, Di Pierro M, Onuchic JN. Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion. Nucleic Acids Research. 50: 4258-4271. PMID 35420130 DOI: 10.1093/nar/gkac231  0.136
1999 Onuchic JN, Wang J, Wolynes PG. Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions Chemical Physics. 247: 175-184.  0.131
2024 Kang TY, Bocci F, Nie Q, Onuchic JN, Levchenko A. Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification. Elife. 12. PMID 38376371 DOI: 10.7554/eLife.89262  0.12
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  0.105
2022 Galbraith M, Bocci F, Onuchic JN. Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway. Plos Computational Biology. 18: e1010306. PMID 35862460 DOI: 10.1371/journal.pcbi.1010306  0.105
2021 Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, ... ... Onuchic JN, et al. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science (New York, N.Y.). 372: 984-989. PMID 34045355 DOI: 10.1126/science.abe2218  0.094
1997 Pande VS, Onuchic JN. Electron transport in disordered polymeric and biological systems Physical Review Letters. 78: 146-149.  0.05
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