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Peter G. Wolynes - Publications

Affiliations: 
CTBP Rice University, Houston, TX 
Area:
protein folding, regulatory networks, glasses, many-body phenomena
Website:
http://chemistry.rice.edu/FacultyDetail.aspx?p=ACC7DC090095C11C

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

Year Citation  Score
2021 Rausch AO, Freiberger MI, Leonetti CO, Luna DM, Radusky LG, Wolynes PG, Ferreiro DU, Gonzalo Parra R. FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations. Bioinformatics (Oxford, England). PMID 33720293 DOI: 10.1093/bioinformatics/btab176  1
2021 Freiberger MI, Wolynes PG, Ferreiro DU, Fuxreiter M. Frustration in Fuzzy Protein Complexes Leads to Interaction Versatility. The Journal of Physical Chemistry. B. 125: 2513-2520. PMID 33667107 DOI: 10.1021/acs.jpcb.0c11068  1
2021 Lu W, Bueno C, Schafer NP, Moller J, Jin S, Chen X, Chen M, Gu X, Davtyan A, de Pablo JJ, Wolynes PG. OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. Plos Computational Biology. 17: e1008308. PMID 33577557 DOI: 10.1371/journal.pcbi.1008308  0.84
2021 Gianni S, Freiberger MI, Jemth P, Ferreiro DU, Wolynes PG, Fuxreiter M. Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly. Accounts of Chemical Research. PMID 33550810 DOI: 10.1021/acs.accounts.0c00813  1
2021 Shen JL, Tsai MY, Schafer NP, Wolynes PG. Modeling Protein Aggregation Kinetics: The Method of Second Stochasticization. The Journal of Physical Chemistry. B. PMID 33476161 DOI: 10.1021/acs.jpcb.0c10331  0.8
2020 Thadani NN, Zhou Q, Gamas KR, Butler S, Bueno C, Schafer NP, Morcos F, Wolynes PG, Suh J. Frustration and Direct Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus. Biophysical Journal. PMID 33359833 DOI: 10.1016/j.bpj.2020.12.018  0.8
2020 Jin S, Miller MD, Chen M, Schafer NP, Lin X, Chen X, Phillips GN, Wolynes PG. Molecular-replacement phasing using predicted protein structures from . Iucrj. 7: 1168-1178. PMID 33209327 DOI: 10.1107/S2052252520013494  0.84
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  1
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  1
2020 Lubchenko V, Wolynes PG. Photon activation of glassy dynamics: A mechanism for photoinduced fluidization, aging, and information storage in amorphous materials. The Journal of Physical Chemistry. B. PMID 32857509 DOI: 10.1021/Acs.Jpcb.0C06515  1
2020 Gu X, Schafer NP, Wang Q, Song SS, Chen M, Waxham MN, Wolynes PG. Exploring the F-actin/CPEB3 interaction and its possible role in the molecular mechanism of long-term memory. Proceedings of the National Academy of Sciences of the United States of America. PMID 32848053 DOI: 10.1073/Pnas.2012964117  0.84
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  1
2020 Jin S, Contessoto VG, Chen M, Schafer NP, Lu W, Chen X, Bueno C, Hajitaheri A, Sirovetz BJ, Davtyan A, Papoian GA, Tsai MY, Wolynes PG. AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes. Nucleic Acids Research. PMID 32383764 DOI: 10.1093/Nar/Gkaa356  1
2020 Liman J, Bueno C, Eliaz Y, Schafer NP, Waxham MN, Wolynes PG, Levine H, Cheung MS. The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks. Proceedings of the National Academy of Sciences of the United States of America. PMID 32354995 DOI: 10.1073/Pnas.1922494117  0.8
2020 Chen X, Chen M, Schafer NP, Wolynes PG. Exploring the interplay between fibrillization and amorphous aggregation channels on the energy landscapes of tau repeat isoforms. Proceedings of the National Academy of Sciences of the United States of America. PMID 32029593 DOI: 10.1073/Pnas.1921702117  0.84
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  1
2019 Tsai MY, Zheng W, Chen M, Wolynes PG. Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation. Journal of the American Chemical Society. PMID 31566963 DOI: 10.1021/Jacs.9B08287  0.84
2019 Wang Q, Chen M, Schafer NP, Bueno C, Song SS, Hudmon A, Wolynes PG, Waxham MN, Cheung MS. Assemblies of calcium/calmodulin-dependent kinase II with actin and their dynamic regulation by calmodulin in dendritic spines. Proceedings of the National Academy of Sciences of the United States of America. PMID 31455737 DOI: 10.1073/Pnas.1911452116  0.84
2019 Xu Y, Safari MS, Ma W, Schafer NP, Wolynes PG, Vekilov PG. Steady, Symmetric, and Reversible Growth and Dissolution of Individual Amyloid-β Fibrils. Acs Chemical Neuroscience. PMID 31099555 DOI: 10.1021/Acschemneuro.9B00179  0.8
2019 Chen J, Schafer NP, Wolynes PG, Clementi C. Localizing Frustration in Proteins Using All-Atom Energy Functions. The Journal of Physical Chemistry. B. PMID 31063375 DOI: 10.1021/Acs.Jpcb.9B01545  0.8
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  1
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, ... Wolynes PG, 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  1
2019 Freiberger MI, Guzovsky AB, Wolynes PG, Parra RG, Ferreiro DU. Local frustration around enzyme active sites. Proceedings of the National Academy of Sciences of the United States of America. PMID 30765513 DOI: 10.1073/Pnas.1819859116  1
2018 Lu W, Schafer NP, Wolynes PG. Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer. Nature Communications. 9: 4949. PMID 30470737 DOI: 10.1038/S41467-018-07320-9  0.84
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  1
2018 Chen M, Schafer NP, Wolynes PG. Surveying the Energy Landscapes of Αβ Fibril Polymorphism. The Journal of Physical Chemistry. B. PMID 30215519 DOI: 10.1021/Acs.Jpcb.8B07364  0.84
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  1
2018 Wang Z, Potoyan DA, Wolynes PG. Modeling the therapeutic efficacy of NFκB synthetic decoy oligodeoxynucleotides (ODNs). Bmc Systems Biology. 12: 4. PMID 29382384 DOI: 10.1186/S12918-018-0525-6  1
2018 Wang Z, Potoyan DA, Wolynes PG. Stochastic resonances in a distributed genetic broadcasting system: the NFκB/IκB paradigm. Journal of the Royal Society, Interface. 15. PMID 29343631 DOI: 10.1098/Rsif.2017.0809  1
2017 Potoyan DA, Wolynes PG. Stochastic dynamics of genetic broadcasting networks. Physical Review. E. 96: 052305. PMID 29347696 DOI: 10.1016/J.Bpj.2016.11.3080  1
2017 Chen M, Schafer NP, Zheng W, Wolynes PG. The AWSEM-Amylometer: predicting amyloid propensity and fibril topology using an optimized folding landscape model. Acs Chemical Neuroscience. PMID 29241326 DOI: 10.1021/Acschemneuro.7B00436  0.84
2017 Lubchenko V, Wolynes PG. Aging, Jamming, and the Limits of Stability of Amorphous Solids. The Journal of Physical Chemistry. B. PMID 29216433 DOI: 10.1021/Acs.Jpcb.7B09553  1
2017 Potoyan DA, Bueno C, Zheng W, Komives EA, Wolynes PG. Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors. Journal of the American Chemical Society. PMID 29183131 DOI: 10.1021/Jacs.7B08741  1
2017 Ferreiro DU, Komives EA, Wolynes PG. Frustration, function and folding. Current Opinion in Structural Biology. 48: 68-73. PMID 29101782 DOI: 10.1016/J.Sbi.2017.09.006  1
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  1
2017 Zheng W, Tsai MY, Wolynes PG. Comparing the Aggregation Free Energy Landscapes of Amyloid Beta(1-42) and Amyloid Beta(1-40). Journal of the American Chemical Society. PMID 29057654 DOI: 10.1021/Jacs.7B08089  0.76
2017 Sirovetz BJ, Schafer NP, Wolynes PG. Protein Structure Prediction: Making AWSEM AWSEM-ER by Adding Evolutionary Restraints. Proteins. PMID 28799172 DOI: 10.1002/Prot.25367  0.8
2017 Chen M, Wolynes PG. Aggregation landscapes of Huntingtin exon 1 protein fragments and the critical repeat length for the onset of Huntington's disease. Proceedings of the National Academy of Sciences of the United States of America. PMID 28400517 DOI: 10.1073/Pnas.1702237114  0.84
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  1
2016 Chen M, Tsai M, Zheng W, Wolynes PG. The Aggregation Free Energy Landscapes of Polyglutamine Repeats. Journal of the American Chemical Society. PMID 27786478 DOI: 10.1021/Jacs.6B08665  0.84
2016 Zheng W, Tsai MY, Chen M, Wolynes PG. Exploring the aggregation free energy landscape of the amyloid-β protein (1-40). Proceedings of the National Academy of Sciences of the United States of America. PMID 27698130 DOI: 10.1073/Pnas.1612362113  0.84
2016 Zhang B, Wolynes PG. Genomic Energy Landscapes. Biophysical Journal. PMID 27692923 DOI: 10.1016/J.Bpj.2016.08.046  1
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  1
2016 Tsai M, Zhang B, Zheng W, Wolynes PG. The Molecular Mechanism of Facilitated Dissociation of Fis Protein from DNA. Journal of the American Chemical Society. PMID 27685351 DOI: 10.1021/Jacs.6B08416  1
2016 Wang Z, Potoyan DA, Wolynes PG. Molecular stripping, targets and decoys as modulators of oscillations in the NF-κB/IκBα/DNA genetic network. Journal of the Royal Society, Interface. 13. PMID 27683001 DOI: 10.1098/Rsif.2016.0606  1
2016 Zhang B, Wolynes PG. Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome. Physical Review Letters. 116: 248101. PMID 27367409 DOI: 10.1103/Physrevlett.116.248101  1
2016 Zhang B, Zheng W, Papoian GA, Wolynes PG. Exploring the Free Energy Landscape of Nucleosomes. Journal of the American Chemical Society. PMID 27300314 DOI: 10.1021/Jacs.6B02893  1
2016 Chen M, Lin X, Zheng W, Onuchic JN, Wolynes PG. Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model (AAWSEM). The Journal of Physical Chemistry. B. PMID 27148634 DOI: 10.1021/Acs.Jpcb.6B02451  1
2016 Parra RG, Schafer NP, Radusky LG, Tsai MY, Guzovsky AB, Wolynes PG, Ferreiro DU. Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics. Nucleic Acids Research. PMID 27131359 DOI: 10.1093/Nar/Gkw304  1
2016 Potoyan DA, Zheng W, Ferreiro DU, Wolynes PG, Komives EA. PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites. The Journal of Physical Chemistry. B. PMID 27098223 DOI: 10.1021/Acs.Jpcb.6B02359  1
2016 Chen M, Zheng W, Wolynes PG. Energy landscapes of a mechanical prion and their implications for the molecular mechanism of long-term memory. Proceedings of the National Academy of Sciences of the United States of America. PMID 27091989 DOI: 10.1073/Pnas.1602702113  1
2016 Trelle MB, Ramsey KM, Lee TC, Zheng W, Lamboy J, Wolynes PG, Deniz A, Komives EA. Binding of NFκB Appears to Twist the Ankyrin Repeat Domain of IκBα. Biophysical Journal. 110: 887-95. PMID 26910425 DOI: 10.1016/J.Bpj.2016.01.001  0.84
2016 Schafer NP, Truong HH, Otzen DE, Lindorff-Larsen K, Wolynes PG. Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease. Proceedings of the National Academy of Sciences of the United States of America. PMID 26858402 DOI: 10.1073/Pnas.1524027113  0.8
2015 Truong HH, Kim BL, Schafer NP, Wolynes PG. Predictive energy landscapes for folding membrane protein assemblies. The Journal of Chemical Physics. 143: 243101. PMID 26723586 DOI: 10.1063/1.4929598  0.8
2015 Potoyan DA, Zheng W, Komives EA, Wolynes PG. Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network. Proceedings of the National Academy of Sciences of the United States of America. PMID 26699500 DOI: 10.1073/Pnas.1520483112  1
2015 Potoyan DA, Wolynes PG. Dichotomous noise models of gene switches. The Journal of Chemical Physics. 143: 195101. PMID 26590554 DOI: 10.1063/1.4935572  1
2015 Bai X, Wolynes PG. On the hydrodynamics of swimming enzymes. The Journal of Chemical Physics. 143: 165101. PMID 26520553 DOI: 10.1063/1.4933424  0.4
2015 Tsai MY, Zheng W, Balamurugan D, Schafer NP, Kim BL, Cheung MS, Wolynes PG. Electrostatics, Structure Prediction and the Energy Landscapes for Protein Folding and Binding. Protein Science : a Publication of the Protein Society. PMID 26183799 DOI: 10.1002/Pro.2751  1
2015 Sirovetz BJ, Schafer NP, Wolynes PG. Water Mediated Interactions and the Protein Folding Phase Diagram in the Temperature-Pressure Plane. The Journal of Physical Chemistry. B. PMID 26102155 DOI: 10.1021/Acs.Jpcb.5B03828  0.8
2015 Zhang B, Wolynes PG. Topology, structures, and energy landscapes of human chromosomes. Proceedings of the National Academy of Sciences of the United States of America. 112: 6062-7. PMID 25918364 DOI: 10.1073/Pnas.1506257112  1
2015 Ashfold M, Parker D, Brown W, Nussinov R, Wolynes PG, Messinger J, Lubitz W, Shen JR, Koper MTM, Iwasawa Y. PCCP-A society journal going from strength to strength Physical Chemistry Chemical Physics. 17: 23-25. DOI: 10.1039/C4Cp90182G  1
2014 Schafer NP, Kim BL, Zheng W, Wolynes PG. Learning To Fold Proteins Using Energy Landscape Theory. Israel Journal of Chemistry. 54: 1311-1337. PMID 25308991 DOI: 10.1002/Ijch.201300145  0.8
2014 Ferreiro DU, Komives EA, Wolynes PG. Frustration in biomolecules. Quarterly Reviews of Biophysics. 47: 285-363. PMID 25225856 DOI: 10.1017/S0033583514000092  1
2014 Morcos F, Schafer NP, Cheng RR, Onuchic JN, Wolynes PG. Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection. Proceedings of the National Academy of Sciences of the United States of America. 111: 12408-13. PMID 25114242 DOI: 10.1073/Pnas.1413575111  1
2014 Kim BL, Schafer NP, Wolynes PG. Predictive energy landscapes for folding α-helical transmembrane proteins. Proceedings of the National Academy of Sciences of the United States of America. 111: 11031-6. PMID 25030446 DOI: 10.1073/Pnas.1410529111  0.8
2014 Zhang B, Wolynes PG. Stem cell differentiation as a many-body problem. Proceedings of the National Academy of Sciences of the United States of America. 111: 10185-90. PMID 24946805 DOI: 10.1073/Pnas.1408561111  1
2014 Wisitsorasak A, Wolynes PG. Dynamical heterogeneity of the glassy state. The Journal of Physical Chemistry. B. 118: 7835-47. PMID 24811573 DOI: 10.1021/Jp4125777  0.01
2014 Potoyan DA, Wolynes PG. On the dephasing of genetic oscillators. Proceedings of the National Academy of Sciences of the United States of America. 111: 2391-6. PMID 24469814 DOI: 10.1073/Pnas.1323433111  1
2013 Wang S, Wolynes PG. Active patterning and asymmetric transport in a model actomyosin network. The Journal of Chemical Physics. 139: 235103. PMID 24359394 DOI: 10.1063/1.4848657  0.64
2013 Zheng W, Schafer NP, Wolynes PG. Free energy landscapes for initiation and branching of protein aggregation. Proceedings of the National Academy of Sciences of the United States of America. 110: 20515-20. PMID 24284165 DOI: 10.1073/Pnas.1320483110  0.8
2013 Rabochiy P, Wolynes PG, Lubchenko V. Microscopically based calculations of the free energy barrier and dynamic length scale in supercooled liquids: the comparative role of configurational entropy and elasticity. The Journal of Physical Chemistry. B. 117: 15204-19. PMID 24195747 DOI: 10.1021/Jp409502K  1
2013 Tsytlonok M, Craig PO, Sivertsson E, Serquera D, Perrett S, Best RB, Wolynes PG, Itzhaki LS. Complex energy landscape of a giant repeat protein. Structure (London, England : 1993). 21: 1954-65. PMID 24120762 DOI: 10.1016/J.Str.2013.08.028  1
2013 Truong HH, Kim BL, Schafer NP, Wolynes PG. Funneling and frustration in the energy landscapes of some designed and simplified proteins. The Journal of Chemical Physics. 139: 121908. PMID 24089720 DOI: 10.1063/1.4813504  0.8
2013 Wang S, Wolynes PG. Microscopic theory of the glassy dynamics of passive and active network materials. The Journal of Chemical Physics. 138: 12A521. PMID 23556772 DOI: 10.1063/1.4773349  0.64
2013 Zheng W, Schafer NP, Wolynes PG. Frustration in the energy landscapes of multidomain protein misfolding. Proceedings of the National Academy of Sciences of the United States of America. 110: 1680-5. PMID 23319605 DOI: 10.1073/Pnas.1222130110  0.8
2013 Schafer NP, Hoffman RMB, Burger A, Craig PO, Komives EA, Wolynes PG. Correction: Discrete kinetic models from funneled energy landscape simulations (PLoS ONE) Plos One. 8. DOI: 10.1371/Annotation/16C11A12-4245-403C-80Ab-E6662Baf16Cd  1
2012 Schafer NP, Hoffman RM, Burger A, Craig PO, Komives EA, Wolynes PG. Discrete kinetic models from funneled energy landscape simulations. Plos One. 7: e50635. PMID 23251375 DOI: 10.1371/Journal.Pone.0050635  1
2012 Burger A, Walczak AM, Wolynes PG. Influence of decoys on the noise and dynamics of gene expression. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 041920. PMID 23214628 DOI: 10.1103/Physreve.86.041920  1
2012 Zheng W, Schafer NP, Davtyan A, Papoian GA, Wolynes PG. Predictive energy landscapes for protein-protein association. Proceedings of the National Academy of Sciences of the United States of America. 109: 19244-9. PMID 23129648 DOI: 10.1073/Pnas.1216215109  1
2012 Wolynes PG, Eaton WA, Fersht AR. Chemical physics of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 109: 17770-1. PMID 23112193 DOI: 10.1073/Pnas.1215733109  1
2012 Jenik M, Parra RG, Radusky LG, Turjanski A, Wolynes PG, Ferreiro DU. Protein frustratometer: a tool to localize energetic frustration in protein molecules. Nucleic Acids Research. 40: W348-51. PMID 22645321 DOI: 10.1093/Nar/Gks447  1
2012 Davtyan A, Schafer NP, Zheng W, Clementi C, Wolynes PG, Papoian GA. AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing. The Journal of Physical Chemistry. B. 116: 8494-503. PMID 22545654 DOI: 10.1021/Jp212541Y  1
2012 Wang S, Wolynes PG. Tensegrity and motor-driven effective interactions in a model cytoskeleton. The Journal of Chemical Physics. 136: 145102. PMID 22502548 DOI: 10.1063/1.3702583  0.64
2012 Wang S, Wolynes PG. Active contractility in actomyosin networks. Proceedings of the National Academy of Sciences of the United States of America. 109: 6446-51. PMID 22493220 DOI: 10.1073/Pnas.1204205109  0.64
2012 Lammert H, Wolynes PG, Onuchic JN. The role of atomic level steric effects and attractive forces in protein folding. Proteins. 80: 362-73. PMID 22081451 DOI: 10.1002/Prot.23187  1
2012 Dzero M, Schmalian J, Wolynes PG. Glassiness in Uniformly Frustrated Systems Structural Glasses and Supercooled Liquids: Theory, Experiment, and Applications. 193-221. DOI: 10.1002/9781118202470.ch5  1
2012 Lubchenko V, Wolynes PG. Theories of Structural Glass Dynamics: Mosaics, Jamming, and All That Structural Glasses and Supercooled Liquids: Theory, Experiment, and Applications. 341-379. DOI: 10.1002/9781118202470.ch10  1
2012 Wolynes PG, Lubchenko V. Structural Glasses and Supercooled Liquids: Theory, Experiment, and Applications Structural Glasses and Supercooled Liquids: Theory, Experiment, and Applications. DOI: 10.1002/9781118202470  1
2011 Craig PO, Lätzer J, Weinkam P, Hoffman RM, Ferreiro DU, Komives EA, Wolynes PG. Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. Journal of the American Chemical Society. 133: 17463-72. PMID 21913704 DOI: 10.1021/Ja207506Z  1
2011 Wang S, Wolynes PG. On the spontaneous collective motion of active matter. Proceedings of the National Academy of Sciences of the United States of America. 108: 15184-9. PMID 21876141 DOI: 10.1073/Pnas.1112034108  0.64
2011 Wang S, Wolynes PG. Communication: Effective temperature and glassy dynamics of active matter. The Journal of Chemical Physics. 135: 051101. PMID 21823683 DOI: 10.1063/1.3624753  0.64
2011 Li W, Wolynes PG, Takada S. Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins. Proceedings of the National Academy of Sciences of the United States of America. 108: 3504-9. PMID 21307307 DOI: 10.1073/Pnas.1018983108  0.68
2011 Ferreiro DU, Hegler JA, Komives EA, Wolynes PG. On the role of frustration in the energy landscapes of allosteric proteins. Proceedings of the National Academy of Sciences of the United States of America. 108: 3499-503. PMID 21273505 DOI: 10.1073/Pnas.1018980108  1
2011 Wang S, Shen T, Wolynes PG. The interplay of nonlinearity and architecture in equilibrium cytoskeletal mechanics. The Journal of Chemical Physics. 134: 014510. PMID 21219010 DOI: 10.1063/1.3518450  1
2011 Stevenson JD, Wolynes PG. The ultimate fate of supercooled liquids. The Journal of Physical Chemistry. A. 115: 3713-9. PMID 21171637 DOI: 10.1021/Jp1060057  1
2011 Kurchan J, Langer JS, Witten TA, Wolynes PG. Scientific interview Dynamical Heterogeneities in Glasses, Colloids, and Granular Media. DOI: 10.1093/acprof:oso/9780199691470.003.0001  1
2010 Prentiss MC, Wales DJ, Wolynes PG. The energy landscape, folding pathways and the kinetics of a knotted protein. Plos Computational Biology. 6: e1000835. PMID 20617197 DOI: 10.1371/Journal.Pcbi.1000835  1
2010 Oklejas V, Zong C, Papoian GA, Wolynes PG. Protein structure prediction: do hydrogen bonding and water-mediated interactions suffice? Methods (San Diego, Calif.). 52: 84-90. PMID 20561998 DOI: 10.1016/J.Ymeth.2010.05.006  1
2010 Bhattacharyya SM, Bagchi B, Wolynes PG. Subquadratic wavenumber dependence of the structural relaxation of supercooled liquid in the crossover regime. The Journal of Chemical Physics. 132: 104503. PMID 20232967 DOI: 10.1063/1.3330911  1
2010 Burger A, Walczak AM, Wolynes PG. Abduction and asylum in the lives of transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 107: 4016-21. PMID 20160109 DOI: 10.1073/Pnas.0915138107  1
2010 Weinkam P, Zimmermann J, Romesberg FE, Wolynes PG. The folding energy landscape and free energy excitations of cytochrome c. Accounts of Chemical Research. 43: 652-60. PMID 20143816 DOI: 10.1021/Ar9002703  1
2010 Trizac E, Levy Y, Wolynes PG. Capillarity theory for the fly-casting mechanism. Proceedings of the National Academy of Sciences of the United States of America. 107: 2746-50. PMID 20133683 DOI: 10.1073/Pnas.0914727107  0.72
2009 Stevenson JD, Wolynes PG. A universal origin for secondary relaxations in supercooled liquids and structural glasses. Nature Physics. 6: 62-68. PMID 20336168 DOI: 10.1038/Nphys1432  1
2009 Lenz P, Cho SS, Wolynes PG. Analysis of single molecule folding studies with replica correlation functions. Chemical Physics Letters. 471: 310-314. PMID 20161316 DOI: 10.1016/J.Cplett.2009.02.054  1
2009 Schultz D, Wolynes PG, Ben Jacob E, Onuchic JN. Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America. 106: 21027-34. PMID 19995980 DOI: 10.1073/Pnas.0912185106  1
2009 Hegler JA, Lätzer J, Shehu A, Clementi C, Wolynes PG. Restriction versus guidance in protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 106: 15302-7. PMID 19706384 DOI: 10.1073/Pnas.0907002106  1
2009 Walczak AM, Wolynes PG. Gene-gene cooperativity in small networks. Biophysical Journal. 96: 4525-41. PMID 19486675 DOI: 10.1016/J.Bpj.2009.03.005  1
2009 Wang W, Xu WX, Levy Y, Trizac E, Wolynes PG. Confinement effects on the kinetics and thermodynamics of protein dimerization. Proceedings of the National Academy of Sciences of the United States of America. 106: 5517-22. PMID 19297622 DOI: 10.1073/Pnas.0809649106  0.72
2009 Weinkam P, Romesberg FE, Wolynes PG. Chemical frustration in the protein folding landscape: grand canonical ensemble simulations of cytochrome c. Biochemistry. 48: 2394-402. PMID 19199810 DOI: 10.1021/Bi802293M  1
2009 Weinkam P, Pletneva EV, Gray HB, Winkler JR, Wolynes PG. Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles. Proceedings of the National Academy of Sciences of the United States of America. 106: 1796-801. PMID 19181849 DOI: 10.1073/Pnas.0813120106  1
2009 Cho SS, Levy Y, Wolynes PG. Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics. Proceedings of the National Academy of Sciences of the United States of America. 106: 434-9. PMID 19075236 DOI: 10.1073/Pnas.0810218105  1
2009 Dzero M, Schmalian J, Wolynes PG. Replica theory for fluctuations of the activation barriers in glassy systems Physical Review B - Condensed Matter and Materials Physics. 80. DOI: 10.1103/Physrevb.80.024204  1
2008 Hegler JA, Weinkam P, Wolynes PG. The spectrum of biomolecular states and motions. Hfsp Journal. 2: 307-13. PMID 19436496 DOI: 10.2976/1.3003931  1
2008 Whitford PC, Onuchic JN, Wolynes PG. Energy landscape along an enzymatic reaction trajectory: hinges or cracks? Hfsp Journal. 2: 61-4. PMID 19404472 DOI: 10.2976/1.2894846  1
2008 Stevenson JD, Wolynes PG. On the surface of glasses. The Journal of Chemical Physics. 129: 234514. PMID 19102545 DOI: 10.1063/1.3041651  1
2008 Weinkam P, Zimmermann J, Sagle LB, Matsuda S, Dawson PE, Wolynes PG, Romesberg FE. Characterization of alkaline transitions in ferricytochrome c using carbon-deuterium infrared probes. Biochemistry. 47: 13470-80. PMID 19035653 DOI: 10.1021/Bi801223N  1
2008 Schultz D, Walczak AM, Onuchic JN, Wolynes PG. Extinction and resurrection in gene networks. Proceedings of the National Academy of Sciences of the United States of America. 105: 19165-70. PMID 19033463 DOI: 10.1073/Pnas.0810366105  1
2008 Stevenson JD, Walczak AM, Hall RW, Wolynes PG. Constructing explicit magnetic analogies for the dynamics of glass forming liquids. The Journal of Chemical Physics. 129: 194505. PMID 19026064 DOI: 10.1063/1.3009827  1
2008 Bhattacharyya SM, Bagchi B, Wolynes PG. Facilitation, complexity growth, mode coupling, and activated dynamics in supercooled liquids. Proceedings of the National Academy of Sciences of the United States of America. 105: 16077-82. PMID 18927234 DOI: 10.1073/Pnas.0808375105  1
2008 Ferreiro DU, Wolynes PG. The capillarity picture and the kinetics of one-dimensional protein folding. Proceedings of the National Academy of Sciences of the United States of America. 105: 9853-4. PMID 18632565 DOI: 10.1073/Pnas.0805287105  1
2008 Prentiss MC, Wales DJ, Wolynes PG. Protein structure prediction using basin-hopping. The Journal of Chemical Physics. 128: 225106. PMID 18554063 DOI: 10.1063/1.2929833  1
2008 Ferreiro DU, Walczak AM, Komives EA, Wolynes PG. The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. Plos Computational Biology. 4: e1000070. PMID 18483553 DOI: 10.1371/Journal.Pcbi.1000070  1
2008 Shen T, Zong C, Portman JJ, Wolynes PG. Variationally determined free energy profiles for structural models of proteins: characteristic temperatures for folding and trapping. The Journal of Physical Chemistry. B. 112: 6074-82. PMID 18376882 DOI: 10.1021/Jp076280N  1
2008 Lätzer J, Shen T, Wolynes PG. Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles. Biochemistry. 47: 2110-22. PMID 18198897 DOI: 10.1021/Bi701350V  1
2008 Cho SS, Weinkam P, Wolynes PG. Origins of barriers and barrierless folding in BBL. Proceedings of the National Academy of Sciences of the United States of America. 105: 118-23. PMID 18172203 DOI: 10.1073/Pnas.0709376104  1
2008 Hall RW, Wolynes PG. Intermolecular forces and the glass transition. The Journal of Physical Chemistry. B. 112: 301-12. PMID 17990867 DOI: 10.1021/Jp075017J  1
2008 Kwac K, Wolynes PG. Protein structure prediction using an associated memory Hamiltonian and all-atom molecular dynamics simulations Bulletin of the Korean Chemical Society. 29: 2172-2182.  1
2007 Sutto L, Lätzer J, Hegler JA, Ferreiro DU, Wolynes PG. Consequences of localized frustration for the folding mechanism of the IM7 protein. Proceedings of the National Academy of Sciences of the United States of America. 104: 19825-30. PMID 18077415 DOI: 10.1073/Pnas.0709922104  1
2007 Ferreiro DU, Hegler JA, Komives EA, Wolynes PG. Localizing frustration in native proteins and protein assemblies. Proceedings of the National Academy of Sciences of the United States of America. 104: 19819-24. PMID 18077414 DOI: 10.1073/Pnas.0709915104  1
2007 Lu T, Shen T, Bennett MR, Wolynes PG, Hasty J. Phenotypic variability of growing cellular populations. Proceedings of the National Academy of Sciences of the United States of America. 104: 18982-7. PMID 18025471 DOI: 10.1073/Pnas.0706115104  1
2007 Schultz D, Ben Jacob E, Onuchic JN, Wolynes PG. Molecular level stochastic model for competence cycles in Bacillus subtilis. Proceedings of the National Academy of Sciences of the United States of America. 104: 17582-7. PMID 17962411 DOI: 10.1073/Pnas.0707965104  1
2007 Gruebele M, Wolynes PG. Quantizing Ulam's control conjecture. Physical Review Letters. 99: 060201. PMID 17930806 DOI: 10.1103/Physrevlett.99.060201  1
2007 Schultz D, Onuchic JN, Wolynes PG. Understanding stochastic simulations of the smallest genetic networks. The Journal of Chemical Physics. 126: 245102. PMID 17614590 DOI: 10.1063/1.2741544  1
2007 Zong C, Wilson CJ, Shen T, Wittung-Stafshede P, Mayo SL, Wolynes PG. Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin. Proceedings of the National Academy of Sciences of the United States of America. 104: 3159-64. PMID 17301232 DOI: 10.1073/Pnas.0611149104  1
2007 Lätzer J, Papoian GA, Prentiss MC, Komives EA, Wolynes PG. Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta. Journal of Molecular Biology. 367: 262-74. PMID 17257619 DOI: 10.1016/J.Jmb.2006.12.006  1
2007 Levy Y, Onuchic JN, Wolynes PG. Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition. Journal of the American Chemical Society. 129: 738-9. PMID 17243791 DOI: 10.1021/Ja065531N  1
2007 Ferreiro DU, Cervantes CF, Truhlar SM, Cho SS, Wolynes PG, Komives EA. Stabilizing IkappaBalpha by "consensus" design. Journal of Molecular Biology. 365: 1201-16. PMID 17174335 DOI: 10.1016/J.Jmb.2006.11.044  1
2007 Lubchenko V, Wolynes PG. Theory of structural glasses and supercooled liquids. Annual Review of Physical Chemistry. 58: 235-66. PMID 17067282 DOI: 10.1146/Annurev.Physchem.58.032806.104653  1
2007 Lubchenko V, Wolynes PG. The microscopic quantum theory of low temperature amorphous solids Advances in Chemical Physics. 136: 95-206. DOI: 10.1002/9780470175422.ch3  1
2006 Prentiss MC, Hardin C, Eastwood MP, Zong C, Wolynes PG. Protein Structure Prediction:  The Next Generation. Journal of Chemical Theory and Computation. 2: 705-16. PMID 26626675 DOI: 10.1021/Ct0600058  1
2006 Lätzer J, Eastwood MP, Wolynes PG. Simulation studies of the fidelity of biomolecular structure ensemble recreation. The Journal of Chemical Physics. 125: 214905. PMID 17166047 DOI: 10.1063/1.2375121  0.68
2006 Lu T, Shen T, Zong C, Hasty J, Wolynes PG. Statistics of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space. Proceedings of the National Academy of Sciences of the United States of America. 103: 16752-7. PMID 17071742 DOI: 10.1073/Pnas.0607698103  1
2006 Lan Y, Wolynes PG, Papoian GA. A variational approach to the stochastic aspects of cellular signal transduction. The Journal of Chemical Physics. 125: 124106. PMID 17014165 DOI: 10.1063/1.2353835  1
2006 Okazaki K, Koga N, Takada S, Onuchic JN, Wolynes PG. Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 103: 11844-9. PMID 16877541 DOI: 10.1073/Pnas.0604375103  1
2006 Zong C, Wilson CJ, Shen T, Wolynes PG, Wittung-Stafshede P. Phi-value analysis of apo-azurin folding: comparison between experiment and theory. Biochemistry. 45: 6458-66. PMID 16700556 DOI: 10.1021/Bi060025W  1
2006 Lu T, Hasty J, Wolynes PG. Effective temperature in stochastic kinetics and gene networks. Biophysical Journal. 91: 84-94. PMID 16617067 DOI: 10.1529/Biophysj.105.074914  1
2006 Zong C, Papoian GA, Ulander J, Wolynes PG. Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of alpha/beta proteins. Journal of the American Chemical Society. 128: 5168-76. PMID 16608353 DOI: 10.1021/Ja058589V  1
2006 Zong C, Lu T, Shen T, Wolynes PG. Nonequilibrium self-assembly of linear fibers: microscopic treatment of growth, decay, catastrophe and rescue. Physical Biology. 3: 83-92. PMID 16582473 DOI: 10.1088/1478-3975/3/1/009  1
2006 Cho SS, Levy Y, Wolynes PG. P versus Q: structural reaction coordinates capture protein folding on smooth landscapes. Proceedings of the National Academy of Sciences of the United States of America. 103: 586-91. PMID 16407126 DOI: 10.1073/Pnas.0509768103  1
2006 Shen T, Wolynes PG. Statistical mechanics of a cat's cradle New Journal of Physics. 8. DOI: 10.1088/1367-2630/8/11/273  1
2006 Lubchenko V, Silbey RJ, Wolynes PG. Electrodynamics of amorphous media at low temperatures Molecular Physics. 104: 1325-1335. DOI: 10.1080/00268970500395661  1
2006 Stevenson JD, Schmalian J, Wolynes PG. The shapes of cooperatively rearranging regions in glass-forming liquids Nature Physics. 2: 268-274. DOI: 10.1038/Nphys261  1
2006 Prentiss MC, Hardin C, Eastwood MP, Zong C, Wolynes PG. Protein structure prediction: The next generation Journal of Chemical Theory and Computation. 2: 705-716. DOI: 10.1021/ct0600058  1
2006 Leitner DM, Wolynes PG. Quantum theory of enhanced unimolecular reaction rates below the ergodicity threshold Chemical Physics. 329: 163-167. DOI: 10.1016/J.Chemphys.2006.05.013  1
2005 Stevenson JD, Wolynes PG. Thermodynamic-kinetic correlations in supercooled liquids: a critical survey of experimental data and predictions of the random first-order transition theory of glasses. The Journal of Physical Chemistry. B. 109: 15093-7. PMID 16852910 DOI: 10.1021/Jp052279H  1
2005 Lubchenko V, Wolynes PG, Frauenfelder H. Mosaic energy landscapes of liquids and the control of protein conformational dynamics by glass-forming solvents. The Journal of Physical Chemistry. B. 109: 7488-99. PMID 16851860 DOI: 10.1021/Jp045205Z  1
2005 Miyashita O, Wolynes PG, Onuchic JN. Simple energy landscape model for the kinetics of functional transitions in proteins. The Journal of Physical Chemistry. B. 109: 1959-69. PMID 16851180 DOI: 10.1021/Jp046736Q  1
2005 Hornos JE, Schultz D, Innocentini GC, Wang J, Walczak AM, Onuchic JN, Wolynes PG. Self-regulating gene: an exact solution. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 051907. PMID 16383645 DOI: 10.1103/Physreve.72.051907  1
2005 Shen T, Wolynes PG. Nonequilibrium statistical mechanical models for cytoskeletal assembly: towards understanding tensegrity in cells. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 041927. PMID 16383440 DOI: 10.1103/Physreve.72.041927  1
2005 Walczak AM, Onuchic JN, Wolynes PG. Absolute rate theories of epigenetic stability. Proceedings of the National Academy of Sciences of the United States of America. 102: 18926-31. PMID 16361441 DOI: 10.1073/Pnas.0509547102  1
2005 Ferreiro DU, Cho SS, Komives EA, Wolynes PG. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family. Journal of Molecular Biology. 354: 679-92. PMID 16257414 DOI: 10.1016/J.Jmb.2005.09.078  1
2005 Cho SS, Levy Y, Onuchic JN, Wolynes PG. Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation. Physical Biology. 2: S44-55. PMID 16204848 DOI: 10.1088/1478-3975/2/2/S05  1
2005 Shen T, Zong C, Hamelberg D, McCammon JA, Wolynes PG. The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 19: 1389-95. PMID 16126906 DOI: 10.1096/Fj.04-3590Hyp  1
2005 Weinkam P, Zong C, Wolynes PG. A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments. Proceedings of the National Academy of Sciences of the United States of America. 102: 12401-6. PMID 16116080 DOI: 10.1073/Pnas.0505274102  1
2005 Shen T, Hofmann CP, Oliveberg M, Wolynes PG. Scanning malleable transition state ensembles: comparing theory and experiment for folding protein U1A. Biochemistry. 44: 6433-9. PMID 15850377 DOI: 10.1021/Bi0500170  1
2005 Levy Y, Cho SS, Shen T, Onuchic JN, Wolynes PG. Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. Proceedings of the National Academy of Sciences of the United States of America. 102: 2373-8. PMID 15701699 DOI: 10.1073/Pnas.0409572102  1
2005 Levy Y, Cho SS, Onuchic JN, Wolynes PG. A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. Journal of Molecular Biology. 346: 1121-45. PMID 15701522 DOI: 10.1016/J.Jmb.2004.12.021  1
2005 Wolynes PG. Energy landscapes and solved protein-folding problems. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 363: 453-64; discussion 4. PMID 15664893 DOI: 10.1098/Rsta.2004.1502  1
2005 Walczak AM, Sasai M, Wolynes PG. Self-consistent proteomic field theory of stochastic gene switches. Biophysical Journal. 88: 828-50. PMID 15542546 DOI: 10.1529/Biophysj.104.050666  0.72
2005 Dzero M, Schmalian J, Wolynes PG. Activated events in glasses: The structure of entropic droplets Physical Review B - Condensed Matter and Materials Physics. 72. DOI: 10.1103/Physrevb.72.100201  1
2004 Yang S, Cho SS, Levy Y, Cheung MS, Levine H, Wolynes PG, Onuchic JN. Domain swapping is a consequence of minimal frustration. Proceedings of the National Academy of Sciences of the United States of America. 101: 13786-91. PMID 15361578 DOI: 10.1073/Pnas.0403724101  1
2004 Lubchenko V, Wolynes PG. Theory of aging in structural glasses. The Journal of Chemical Physics. 121: 2852-65. PMID 15291595 DOI: 10.1063/1.1771633  1
2004 Levy Y, Caflisch A, Onuchic JN, Wolynes PG. The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations. Journal of Molecular Biology. 340: 67-79. PMID 15184023 DOI: 10.1016/J.Jmb.2004.04.028  1
2004 Shen T, Wolynes PG. Stability and dynamics of crystals and glasses of motorized particles. Proceedings of the National Academy of Sciences of the United States of America. 101: 8547-50. PMID 15173584 DOI: 10.1073/Pnas.0402602101  1
2004 Onuchic JN, Wolynes PG. Theory of protein folding. Current Opinion in Structural Biology. 14: 70-5. PMID 15102452 DOI: 10.1016/J.Sbi.2004.01.009  1
2004 Gruebele M, Wolynes PG. Vibrational energy flow and chemical reactions. Accounts of Chemical Research. 37: 261-7. PMID 15096063 DOI: 10.1021/Ar030230T  1
2004 Papoian GA, Ulander J, Eastwood MP, Luthey-Schulten Z, Wolynes PG. Water in protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 101: 3352-7. PMID 14988499 DOI: 10.1073/Pnas.0307851100  1
2004 Fujitsuka Y, Takada S, Luthey-Schulten ZA, Wolynes PG. Optimizing physical energy functions for protein folding. Proteins. 54: 88-103. PMID 14705026 DOI: 10.1002/Prot.10429  1
2004 Levy Y, Wolynes PG, Onuchic JN. Protein topology determines binding mechanism. Proceedings of the National Academy of Sciences of the United States of America. 101: 511-6. PMID 14694192 DOI: 10.1073/Pnas.2534828100  1
2004 Levy Y, Papoian GA, Onuchic JN, Wolynes PG. Energy landscape analysis of protein dimers Israel Journal of Chemistry. 44: 281-297. DOI: 10.1560/Xgcb-Wuhn-Jrjc-Bv0Y  1
2004 Wu S, Schmalian J, Kotliar G, Wolynes PG. Solution of local-field equations for self-generated glasses Physical Review B - Condensed Matter and Materials Physics. 70: 024207-1-024207-11. DOI: 10.1103/Physrevb.70.024207  1
2003 Papoian GA, Ulander J, Wolynes PG. Role of water mediated interactions in protein-protein recognition landscapes. Journal of the American Chemical Society. 125: 9170-8. PMID 15369374 DOI: 10.1021/Ja034729U  1
2003 Miyashita O, Onuchic JN, Wolynes PG. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proceedings of the National Academy of Sciences of the United States of America. 100: 12570-5. PMID 14566052 DOI: 10.1073/Pnas.2135471100  1
2003 Plotkin SS, Wolynes PG. Buffed energy landscapes: another solution to the kinetic paradoxes of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 100: 4417-22. PMID 12677002 DOI: 10.1073/Pnas.0330720100  0.52
2003 Hall RW, Wolynes PG. Microscopic theory of network glasses. Physical Review Letters. 90: 085505. PMID 12633439 DOI: 10.1103/Physrevlett.90.085505  1
2003 Papoian GA, Wolynes PG. The physics and bioinformatics of binding and folding-an energy landscape perspective. Biopolymers. 68: 333-49. PMID 12601793 DOI: 10.1002/Bip.10286  1
2003 Lubchenko V, Wolynes PG. The origin of the boson peak and thermal conductivity plateau in low-temperature glasses. Proceedings of the National Academy of Sciences of the United States of America. 100: 1515-8. PMID 12578972 DOI: 10.1073/Pnas.252786999  1
2003 Hardin C, Eastwood MP, Prentiss MC, Luthey-Schulten Z, Wolynes PG. Associative memory Hamiltonians for structure prediction without homology: alpha/beta proteins. Proceedings of the National Academy of Sciences of the United States of America. 100: 1679-84. PMID 12554830 DOI: 10.1073/Pnas.252753899  1
2003 Lubchenko V, Wolynes PG. Barrier softening near the onset of nonactivated transport in supercooled liquids: Implications for establishing detailed connection between thermodynamic and kinetic anomalies in supercooled liquids Journal of Chemical Physics. 119: 9088-9105. DOI: 10.1063/1.1614180  1
2003 Eastwood MP, Hardin C, Luthey-Schulten Z, Wolynes PG. Statistical mechanical refinement of protein structure prediction schemes. II. Mayer cluster expansion approach Journal of Chemical Physics. 118: 8500-8512. DOI: 10.1063/1.1565106  1
2003 Leitner DM, Levine B, Quenneville J, Martínez TJ, Wolynes PG. Quantum energy flow and trans-stilbene photoisomerization: An example of a non-RRKM reaction Journal of Physical Chemistry A. 107: 10706-10716. DOI: 10.1021/Jp0305180  1
2002 Hardin C, Eastwood MP, Prentiss M, Luthey-Schulten Z, Wolynes PG. Folding funnels: the key to robust protein structure prediction. Journal of Computational Chemistry. 23: 138-46. PMID 11913379 DOI: 10.1002/Jcc.1162  1
2002 Eastwood MP, Hardin C, Luthey-Schulten Z, Wolynes PG. Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach Journal of Chemical Physics. 117: 4602-4615. DOI: 10.1063/1.1494417  1
2001 Lubchenko V, Wolynes PG. Intrinsic quantum excitations of low temperature glasses. Physical Review Letters. 87: 195901. PMID 11690429 DOI: 10.1103/Physrevlett.87.195901  1
2001 Xia X, Wolynes PG. Microscopic theory of heterogeneity and nonexponential relaxations in supercooled liquids. Physical Review Letters. 86: 5526-9. PMID 11415292 DOI: 10.1103/Physrevlett.86.5526  1
2001 Portman JJ, Takada S, Wolynes PG. Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics Journal of Chemical Physics. 114: 5082-5096. DOI: 10.1063/1.1334663  1
2001 Portman JJ, Takada S, Wolynes PG. Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach Journal of Chemical Physics. 114: 5069-5081. DOI: 10.1063/1.1334662  1
2000 Hardin C, Eastwood MP, Luthey-Schulten Z, Wolynes PG. Associative memory hamiltonians for structure prediction without homology: alpha-helical proteins. Proceedings of the National Academy of Sciences of the United States of America. 97: 14235-40. PMID 11114172 DOI: 10.1073/pnas.230432197  1
2000 Schmalian J, Wolynes PG. Stripe glasses: self-generated randomness in a uniformly frustrated system Physical Review Letters. 85: 836-9. PMID 10991411 DOI: 10.1103/Physrevlett.85.836  0.52
2000 Shoemaker BA, Portman JJ, Wolynes PG. Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proceedings of the National Academy of Sciences of the United States of America. 97: 8868-73. PMID 10908673 DOI: 10.1073/Pnas.160259697  1
2000 Xia X, Wolynes PG. Fragilities of liquids predicted from the random first order transition theory of glasses. Proceedings of the National Academy of Sciences of the United States of America. 97: 2990-4. PMID 10737779 DOI: 10.1073/Pnas.97.7.2990  1
1999 Bai C, Wang C, Xie XS, Wolynes PG. Single molecule physics and chemistry. Proceedings of the National Academy of Sciences of the United States of America. 96: 11075-6. PMID 10500130 DOI: 10.1073/pnas.96.20.11075  0.68
1999 Shoemaker BA, Wang J, Wolynes PG. Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble. Journal of Molecular Biology. 287: 675-94. PMID 10092467 DOI: 10.1006/Jmbi.1999.2613  1
1999 Shoemaker BA, Wolynes PG. Exploring structures in protein folding funnels with free energy functionals: the denatured ensemble. Journal of Molecular Biology. 287: 657-74. PMID 10092466 DOI: 10.1006/Jmbi.1999.2612  1
1999 Socci ND, Onuchic JN, Wolynes PG. Stretching lattice models of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 96: 2031-5. PMID 10051589 DOI: 10.1073/Pnas.96.5.2031  1
1999 Hardin C, Luthey-Schulten Z, Wolynes PG. Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides. Proteins. 34: 281-94. PMID 10024016 DOI: 10.1002/(Sici)1097-0134(19990215)34:3<281::Aid-Prot2>3.0.Co;2-2  1
1999 Wolynes PG, Eaton WA. The physics of protein folding Physics World. 12: 39-44. DOI: 10.1088/2058-7058/12/9/24  1
1999 Portman JJ, Wolynes PG. Complementary variational approximations for intermittency and reaction dynamics in fluctuating environments Journal of Physical Chemistry A. 103: 10602-10610. DOI: 10.1021/Jp992334K  1
1999 Prince RB, Saven JG, Wolynes PG, Moore JS. Cooperative conformational transitions in phenylene ethynylene oligomers: Chain-length dependence Journal of the American Chemical Society. 121: 3114-3121. DOI: 10.1021/Ja983995I  1
1998 Brooks CL, Gruebele M, Onuchic JN, Wolynes PG. Chemical physics of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 95: 11037-8. PMID 9736683 DOI: 10.1073/pnas.95.19.11037  1
1998 Socci ND, Onuchic JN, Wolynes PG. Protein folding mechanisms and the multidimensional folding funnel. Proteins. 32: 136-58. PMID 9714155 DOI: 10.1002/(Sici)1097-0134(19980801)32:2<136::Aid-Prot2>3.0.Co;2-J  1
1998 Gruebele M, Wolynes PG. Satisfying turns in folding transitions. Nature Structural Biology. 5: 662-5. PMID 9699621 DOI: 10.1038/1354  1
1998 Bigwood R, Gruebele M, Leitner DM, Wolynes PG. The vibrational energy flow transition in organic molecules: theory meets experiment. Proceedings of the National Academy of Sciences of the United States of America. 95: 5960-4. PMID 9600899 DOI: 10.1073/Pnas.95.11.5960  1
1998 Koretke KK, Luthey-Schulten Z, Wolynes PG. Self-consistently optimized energy functions for protein structure prediction by molecular dynamics. Proceedings of the National Academy of Sciences of the United States of America. 95: 2932-7. PMID 9501193 DOI: 10.1073/Pnas.95.6.2932  1
1998 Portman JJ, Takada S, Wolynes PG. Variational theory for site resolved protein folding free energy surfaces Physical Review Letters. 81: 5237-5240. DOI: 10.1103/Physrevlett.81.5237  1
1997 Onuchic JN, Luthey-Schulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annual Review of Physical Chemistry. 48: 545-600. PMID 9348663 DOI: 10.1146/Annurev.Physchem.48.1.545  1
1997 Panchenko AR, Luthey-Schulten Z, Cole R, Wolynes PG. The foldon universe: a survey of structural similarity and self-recognition of independently folding units. Journal of Molecular Biology. 272: 95-105. PMID 9299340 DOI: 10.1006/Jmbi.1997.1205  1
1997 Nelson JC, Saven JG, Moore JS, Wolynes PG. Solvophobically driven folding of nonbiological oligomers. Science (New York, N.Y.). 277: 1793-6. PMID 9295264 DOI: 10.1126/Science.277.5333.1793  1
1997 Haney P, Konisky J, Koretke KK, Luthey-Schulten Z, Wolynes PG. Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus. Proteins. 28: 117-30. PMID 9144797 DOI: 10.1002/(Sici)1097-0134(199705)28:1<117::Aid-Prot12>3.0.Co;2-M  1
1997 Takada S, Portman JJ, Wolynes PG. An elementary mode coupling theory of random heteropolymer dynamics. Proceedings of the National Academy of Sciences of the United States of America. 94: 2318-21. PMID 9122192 DOI: 10.1073/Pnas.94.6.2318  1
1997 Shoemaker BA, Wang J, Wolynes PG. Structural correlations in protein folding funnels. Proceedings of the National Academy of Sciences of the United States of America. 94: 777-82. PMID 9023333 DOI: 10.1073/Pnas.94.3.777  1
1997 Saven JG, Wolynes PG. Statistical mechanics of the combinatorial synthesis and analysis of folding macromolecules Journal of Physical Chemistry B. 101: 8375-8389. DOI: 10.1021/Jp971707J  1
1996 Leitner DM, Wolynes PG. Many-dimensional quantum energy flow at low energy. Physical Review Letters. 76: 216-219. PMID 10061045 DOI: 10.1103/Physrevlett.76.216  1
1996 Plotkin SS, Wang J, Wolynes PG. Correlated energy landscape model for finite, random heteropolymers. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 53: 6271-6296. PMID 9964988 DOI: 10.1103/Physreve.53.6271  0.88
1996 Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG. Protein folding funnels: the nature of the transition state ensemble. Folding & Design. 1: 441-50. PMID 9080190 DOI: 10.1016/S1359-0278(96)00060-0  1
1996 Wolynes PG, Luthey-Schulten Z, Onuchic JN. Fast-folding experiments and the topography of protein folding energy landscapes Chemistry and Biology. 3: 425-432. PMID 8807873 DOI: 10.1016/S1074-5521(96)90090-3  1
1996 Koretke KK, Luthey-Schulten Z, Wolynes PG. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. Protein Science : a Publication of the Protein Society. 5: 1043-59. PMID 8762136 DOI: 10.1002/Pro.5560050607  1
1996 Panchenko AR, Luthey-Schulten Z, Wolynes PG. Foldons, protein structural modules, and exons. Proceedings of the National Academy of Sciences of the United States of America. 93: 2008-13. PMID 8700876 DOI: 10.1073/Pnas.93.5.2008  1
1996 Saven JG, Wolynes PG. Local conformational signals and the statistical thermodynamics of collapsed helical proteins. Journal of Molecular Biology. 257: 199-216. PMID 8632455 DOI: 10.1006/Jmbi.1996.0156  1
1996 Wang J, Saven JG, Wolynes PG. Kinetics in a globally connected, correlated random energy model Journal of Chemical Physics. 105: 11276-11284.  1
1996 Dakhnovskii Y, Lubchenko V, Wolynes P. "False tunneling" and multirelaxation time nonexponential kinetics of electron transfer in polar glasses Journal of Chemical Physics. 104: 1875-1885.  1
1995 Wolynes PG, Onuchic JN, Thirumalai D. Response. Science (New York, N.Y.). 268: 960-1. PMID 17774212 DOI: 10.1126/science.268.5213.960  1
1995 Schofield SA, Wolynes PG, Wyatt RE. Computational study of many-dimensional quantum energy flow: From action diffusion to localization. Physical Review Letters. 74: 3720-3723. PMID 10058280 DOI: 10.1103/Physrevlett.74.3720  1
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  1
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  1
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  1
1994 Frauenfelder H, Wolynes PG. Biomolecules: Where the Physics of Complexity and Simplicity Meet Physics Today. 47: 58-64. DOI: 10.1063/1.881414  0.4
1994 Saven JG, Wang J, Wolynes PG. Kinetics of protein folding: The dynamics of globally connected rough energy landscapes with biases The Journal of Chemical Physics. 101: 11037-11043.  1
1993 Goldstein RA, Katzenellenbogen JA, Luthey-Schulten ZA, Seielstad DA, Wolynes PG. Three-dimensional model for the hormone binding domains of steroid receptors. Proceedings of the National Academy of Sciences of the United States of America. 90: 9949-53. PMID 8234340 DOI: 10.1073/Pnas.90.21.9949  1
1992 Weissman MB, Wolynes PG. Hopfield models and spin-density waves in metallic spin glasses. Physical Review. B, Condensed Matter. 46: 14209-14212. PMID 10003498 DOI: 10.1103/PhysRevB.46.14209  1
1992 Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Optimal protein-folding codes from spin-glass theory. Proceedings of the National Academy of Sciences of the United States of America. 89: 4918-22. PMID 1594594 DOI: 10.1073/Pnas.89.11.4918  1
1992 Goldstein RA, Luthey-Schulten ZA, Wolynes PG. Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proceedings of the National Academy of Sciences of the United States of America. 89: 9029-33. PMID 1409599 DOI: 10.1073/Pnas.89.19.9029  1
1991 Friedrichs MS, Goldstein RA, Wolynes PG. Generalized protein tertiary structure recognition using associative memory Hamiltonians. Journal of Molecular Biology. 222: 1013-34. PMID 1762143 DOI: 10.1016/0022-2836(91)90591-S  1
1991 Frauenfelder H, Sligar SG, Wolynes PG. The energy landscapes and motions of proteins. Science (New York, N.Y.). 254: 1598-603. PMID 1749933 DOI: 10.1126/Science.1749933  1
1991 Zheng C, McCammon JA, Wolynes PG. Quantum simulations of conformation reorganization in the electron transfer reactions of tuna cytochrome c Chemical Physics. 158: 261-270. DOI: 10.1016/0301-0104(91)87070-C  1
1990 Logan DE, Wolynes PG. Quantum localization and energy flow in many-dimensional Fermi resonant systems The Journal of Chemical Physics. 93: 4994-5012. DOI: 10.1063/1.458637  1
1990 Friedrichs MS, Wolynes PG. Molecular dynamics of associative memory hamiltonians for protein tertiary structure recognition Tetrahedron Computer Methodology. 3: 175-190. DOI: 10.1016/0898-5529(90)90051-9  1
1988 Zheng C, Wong CF, McCammon JA, Wolynes PG. Quantum simulation of ferrocytochrome c. Nature. 334: 726-8. PMID 2842687 DOI: 10.1038/334726A0  0.32
1987 Logan DE, Wolynes PG. Localizability and dephasing of dipolar excitons in topologically disordered systems The Journal of Chemical Physics. 87: 7199-7207. DOI: 10.1063/1.453363  1
1987 Hall RW, Wolynes PG. The aperiodic crystal picture and free energy barriers in glasses The Journal of Chemical Physics. 86: 2943-2948. DOI: 10.1063/1.452045  1
1987 Mason BA, Hess K, Cline RE, Wolynes PG. A new technique for the calculation of real-time path integrals and applications to electron transport Superlattices and Microstructures. 3: 421-428. DOI: 10.1016/0749-6036(87)90217-5  1
1986 Hall RW, Wolynes PG. Quantum Monte Carlo study of a lattice-atom model for excitonic fluids. Physical Review. B, Condensed Matter. 33: 7879-7881. PMID 9938177 DOI: 10.1103/Physrevb.33.7879  1
1986 Logan DE, Wolynes PG. Anderson localization in topologically disordered systems: The effects of band structure The Journal of Chemical Physics. 85: 937-948. DOI: 10.1063/1.451249  1
1986 Hall RW, Wolynes PG. G. N. Lewis' atom and quantum Monte Carlo studies of liquids Journal of Statistical Physics. 43: 935-948. DOI: 10.1007/Bf02628321  1
1985 Frauenfelder H, Wolynes PG. Rate theories and puzzles of hemeprotein kinetics. Science (New York, N.Y.). 229: 337-45. PMID 4012322 DOI: 10.1126/Science.4012322  1
1985 Cooper K, Jakobsson E, Wolynes P. The theory of ion transport through membrane channels. Progress in Biophysics and Molecular Biology. 46: 51-96. PMID 2410952 DOI: 10.1016/0079-6107(85)90012-4  1
1985 Hall RW, Wolynes PG. Solvent influence on atomic spectra: The effect of finite size The Journal of Chemical Physics. 83: 3214-3221. DOI: 10.1063/1.449179  1
1984 Logan DE, Wolynes PG. Self-consistent theory of localization in topologically disordered systems Physical Review B. 29: 6560-6562. DOI: 10.1103/Physrevb.29.6560  1
1982 LEVY RM, KARPLUS M, WOLYNES PG. ChemInform Abstract: NMR RELAXATION PARAMETERS IN MOLECULES WITH INTERNAL MOTION: EXACT LANGEVIN TRAJECTORY RESULTS COMPARED WITH SIMPLIFIED RELAXATION MODELS Chemischer Informationsdienst. 13. DOI: 10.1002/chin.198203044  0.56
1981 Schweizer KS, Stratt RM, Chandler D, Wolynes PG. Convenient and accurate discretized path integral methods for equilibrium quantum mechanical calculations The Journal of Chemical Physics. 75: 1347-1364. DOI: 10.1063/1.442141  1
1981 Levy RM, Karplus M, Wolynes PG. NMR relaxation parameters in molecules with internal motion: exact Langevin trajectory results compared with simplified relaxation models Journal of the American Chemical Society. 103: 5998-6011. DOI: 10.1021/Ja00410A002  0.56
1979 McCammon JA, Wolynes PG, Karplus M. Picosecond dynamics of tyrosine side chains in proteins. Biochemistry. 18: 927-42. PMID 427100 DOI: 10.1021/Bi00573A001  1
1979 Skinner JL, Wolynes PG. Derivation of Smoluchowski equations with corrections for Fokker-Planck and BGK collision models Physica a: Statistical Mechanics and Its Applications. 96: 561-572. DOI: 10.1016/0378-4371(79)90013-X  1
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