Year |
Citation |
Score |
2024 |
Lu W, Zhang J, Huang W, Zhang Z, Jia X, Wang Z, Shi L, Li C, Wolynes PG, Zheng S. DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model. Nature Communications. 15: 1071. PMID 38316797 DOI: 10.1038/s41467-024-45461-2 |
0.354 |
|
2023 |
Freiberger MI, Ruiz-Serra V, Pontes C, Romero-Durana M, Galaz-Davison P, Ramírez-Sarmiento CA, Schuster CD, Marti MA, Wolynes PG, Ferreiro DU, Parra RG, Valencia A. Local energetic frustration conservation in protein families and superfamilies. Nature Communications. 14: 8379. PMID 38104123 DOI: 10.1038/s41467-023-43801-2 |
0.657 |
|
2023 |
Chen X, Jin S, Chen M, Bueno C, Wolynes PG. The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor. Proceedings of the National Academy of Sciences of the United States of America. 120: e2216906120. PMID 36730193 DOI: 10.1073/pnas.2216906120 |
0.703 |
|
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 |
0.435 |
|
2022 |
Sanches MN, Parra RG, Viegas RG, Oliveira AB, Wolynes PG, Ferreiro DU, Leite VBP. Resolving the fine structure in the energy landscapes of repeat proteins. Qrb Discovery. 3: e7. PMID 37529289 DOI: 10.1017/qrd.2022.4 |
0.72 |
|
2022 |
Chen Y, Jin S, Zhang M, Hu Y, Wu KL, Chung A, Wang S, Tian Z, Wang Y, Wolynes PG, Xiao H. Unleashing the potential of noncanonical amino acid biosynthesis to create cells with precision tyrosine sulfation. Nature Communications. 13: 5434. PMID 36114189 DOI: 10.1038/s41467-022-33111-4 |
0.693 |
|
2022 |
Jin S, Bueno C, Lu W, Wang Q, Chen M, Chen X, Wolynes PG, Gao Y. Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA. Proceedings of the National Academy of Sciences of the United States of America. 119: e2202239119. PMID 35914145 DOI: 10.1073/pnas.2202239119 |
0.719 |
|
2022 |
Chen X, Tsai MY, Wolynes PG. The Role of Charge Density Coupled DNA Bending in Transcription Factor Sequence Binding Specificity: A Generic Mechanism for Indirect Readout. Journal of the American Chemical Society. PMID 35061392 DOI: 10.1021/jacs.1c11911 |
0.717 |
|
2022 |
Chen X, Lu W, Tsai MY, Jin S, Wolynes PG. Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model. Journal of Biological Physics. PMID 35000062 DOI: 10.1007/s10867-021-09596-3 |
0.824 |
|
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 |
0.45 |
|
2022 |
Guzovsky AB, Schafer NP, Wolynes PG, Ferreiro DU. Localization of Energetic Frustration in Proteins. Methods in Molecular Biology (Clifton, N.J.). 2376: 387-398. PMID 34845622 DOI: 10.1007/978-1-0716-1716-8_22 |
0.685 |
|
2021 |
Xu Y, Knapp K, Le KN, Schafer NP, Safari MS, Davtyan A, Wolynes PG, Vekilov PG. Frustrated peptide chains at the fibril tip control the kinetics of growth of amyloid-β fibrils. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34518234 DOI: 10.1073/pnas.2110995118 |
0.627 |
|
2021 |
Ediger MD, Gruebele M, Lubchenko V, Wolynes PG. Glass Dynamics Deep in the Energy Landscape. The Journal of Physical Chemistry. B. PMID 34357766 DOI: 10.1021/acs.jpcb.1c01739 |
0.665 |
|
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 |
0.702 |
|
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 |
0.676 |
|
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 |
0.821 |
|
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 |
0.7 |
|
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 |
0.73 |
|
2020 |
Chen M, Chen X, Schafer NP, Clementi C, Komives EA, Ferreiro DU, Wolynes PG. Surveying biomolecular frustration at atomic resolution. Nature Communications. 11: 5944. PMID 33230150 DOI: 10.1038/s41467-020-19560-9 |
0.667 |
|
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 |
0.734 |
|
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 |
0.481 |
|
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 |
0.424 |
|
2020 |
Chen M, Chen X, Jin S, Lu W, Lin X, Wolynes PG. Protein Structure Refinement Guided by Atomic Packing Frustration Analysis. The Journal of Physical Chemistry. B. PMID 32931278 DOI: 10.1021/Acs.Jpcb.0C06719 |
0.754 |
|
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 |
0.669 |
|
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 |
0.797 |
|
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 |
0.812 |
|
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 |
0.324 |
|
2020 |
Tsai M, Zheng W, Chen M, Wolynes PG. In Silico Studies on Functional Significance of Multiple Binding Configurations of Bacterial Nucleoid Associated Protein-DNA Assemblies Biophysical Journal. 118: 75a-76a. DOI: 10.1016/J.Bpj.2019.11.586 |
0.735 |
|
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 |
0.744 |
|
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 |
0.76 |
|
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 |
0.429 |
|
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 |
0.789 |
|
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 |
0.787 |
|
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 |
0.712 |
|
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 |
0.579 |
|
2019 |
Kirkpatrick TR, Thirumalai D, Wolynes PG. Scaling concepts for the dynamics of viscous liquids near an ideal glassy state. Physical Review. a, General Physics. 40: 1045-1054. PMID 9902230 DOI: 10.1103/Physreva.40.1045 |
0.496 |
|
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 |
0.416 |
|
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 |
0.591 |
|
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 |
0.366 |
|
2018 |
Wu H, Wolynes PG, Papoian GA. AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins. The Journal of Physical Chemistry. B. PMID 30091924 DOI: 10.1021/Acs.Jpcb.8B05791 |
0.68 |
|
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 |
0.745 |
|
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 |
0.696 |
|
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 |
0.717 |
|
2018 |
Bueno CA, Potoyan DA, Cheng RR, Wolynes PG. Prediction of Changes in Protein Folding Stability Upon Single Residue Mutations Biophysical Journal. 114: 199a. DOI: 10.1016/J.Bpj.2017.11.1114 |
0.34 |
|
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 |
0.683 |
|
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 |
0.395 |
|
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 |
0.691 |
|
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 |
0.71 |
|
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 |
0.686 |
|
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 |
0.51 |
|
2017 |
Eaton WA, Wolynes PG. Theory, simulations, and experiments show that proteins fold by multiple pathways. Proceedings of the National Academy of Sciences of the United States of America. PMID 29087352 DOI: 10.1073/Pnas.1716444114 |
0.414 |
|
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 |
0.75 |
|
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 |
0.461 |
|
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 |
0.359 |
|
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 |
0.599 |
|
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 |
0.74 |
|
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 |
0.765 |
|
2016 |
Zhang B, Wolynes PG. Genomic Energy Landscapes. Biophysical Journal. PMID 27692923 DOI: 10.1016/J.Bpj.2016.08.046 |
0.411 |
|
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 |
0.562 |
|
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 |
0.768 |
|
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 |
0.713 |
|
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 |
0.41 |
|
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 |
0.666 |
|
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 |
0.581 |
|
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 |
0.829 |
|
2016 |
Wolynes P. BIOMOLECULAR FOLDING. Moments of excitement. Science (New York, N.Y.). 352: 150-1. PMID 27124442 DOI: 10.1126/Science.Aaf6626 |
0.392 |
|
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 |
0.783 |
|
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 |
0.378 |
|
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 |
0.426 |
|
2016 |
Wang S, Wolynes P. Glassy Dynamics of Passive and Active Network Materials: A Microscopic Theory Biophysical Journal. 110: 617a. DOI: 10.1016/J.Bpj.2015.11.3310 |
0.304 |
|
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 |
0.392 |
|
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 |
0.714 |
|
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 |
0.682 |
|
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 |
0.785 |
|
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 |
0.353 |
|
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 |
0.389 |
|
2015 |
Zhang B, Wolynes PG. Prediction of Chromosome Conformations with Maximum Entropy Principle Biophysical Journal. 108: 537a. DOI: 10.1016/J.Bpj.2014.11.2947 |
0.396 |
|
2015 |
Potoyan D, Wolynes P. Path Attractors and the Origins of Stochastic Bifrucation and Dephasing in Genetic Networks Biophysical Journal. 108: 464a. DOI: 10.1016/J.Bpj.2014.11.2531 |
0.672 |
|
2014 |
Wolynes PG. Evolution, energy landscapes and the paradoxes of protein folding. Biochimie. PMID 25530262 DOI: 10.1016/J.Biochi.2014.12.007 |
0.475 |
|
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 |
0.453 |
|
2014 |
Ferreiro DU, Komives EA, Wolynes PG. Frustration in biomolecules. Quarterly Reviews of Biophysics. 47: 285-363. PMID 25225856 DOI: 10.1017/S0033583514000092 |
0.734 |
|
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 |
0.592 |
|
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 |
0.435 |
|
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 |
0.35 |
|
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 |
0.37 |
|
2014 |
Nussinov R, Wolynes PG. A second molecular biology revolution? The energy landscapes of biomolecular function. Physical Chemistry Chemical Physics : Pccp. 16: 6321-2. PMID 24608340 DOI: 10.1039/C4Cp90027H |
0.332 |
|
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 |
0.68 |
|
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 |
0.31 |
|
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 |
0.445 |
|
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 |
0.689 |
|
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 |
0.437 |
|
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 |
0.451 |
|
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 |
0.318 |
|
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 |
0.437 |
|
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 |
0.553 |
|
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 |
0.681 |
|
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 |
0.58 |
|
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 |
0.804 |
|
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 |
0.406 |
|
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 |
0.731 |
|
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 |
0.779 |
|
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 |
Boechi L, Oklejas V, Wolynes PG. Membrane Protein Folding: Mechanistic and Kinetic Implications Biophysical Journal. 102: 59a. DOI: 10.1016/J.Bpj.2011.11.351 |
0.408 |
|
2012 |
Davtyan A, Zheng W, Schafer N, Wolynes P, Papoian G. AWSEM-MD: Coarse-Grained Protein Structure Prediction using Physical Potentials and Bioinformatically Based Local Structure Biasing Biophysical Journal. 102: 619a. DOI: 10.1016/J.Bpj.2011.11.3373 |
0.8 |
|
2012 |
Hoffman RM, Berger A, Craig PO, Komives EA, Schafer NP, Wolynes PG. Predicting Folding Rates from Umbrella Sampled Data Biophysical Journal. 102: 457a. DOI: 10.1016/J.Bpj.2011.11.2507 |
0.359 |
|
2012 |
Craig PO, Hoffman RM, Lätzer J, Weinkam P, Komives EA, Wolynes PG. Analysis of Native H/D Exchange Dynamics in EX1/EX2 Conditions using Structure Based Model Simulations Biophysical Journal. 102: 448a. DOI: 10.1016/J.Bpj.2011.11.2459 |
0.811 |
|
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 |
0.637 |
|
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 |
0.617 |
|
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 |
0.822 |
|
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 |
0.401 |
|
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 |
0.722 |
|
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 |
0.374 |
|
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 |
0.629 |
|
2011 |
Wolynes PG. Water Mediated Interactions in Protein Folding and Structure Biophysical Journal. 100: 5a. DOI: 10.1016/J.Bpj.2010.12.238 |
0.409 |
|
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 |
0.595 |
|
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 |
0.728 |
|
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 |
0.342 |
|
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 |
0.547 |
|
2010 |
Itzhaki L, Wolynes P. Nature and nurture in protein folding and binding. Current Opinion in Structural Biology. 20: 1-2. PMID 20144542 DOI: 10.1016/J.Sbi.2010.01.007 |
0.374 |
|
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 |
0.826 |
|
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 |
0.407 |
|
2010 |
Friedrichs MS, Wolynes PG. Toward protein tertiary structure recognition by means of associative memory hamiltonians. Science (New York, N.Y.). 246: 371-3. PMID 17747919 DOI: 10.1126/Science.246.4928.371 |
0.319 |
|
2010 |
Zheng C, McCammon JA, Wolynes PG. Quantum simulation of nuclear rearrangement in electron transfer reactions. Proceedings of the National Academy of Sciences of the United States of America. 86: 6441-4. PMID 16594063 DOI: 10.1073/pnas.86.17.6441 |
0.38 |
|
2010 |
Itzhaki L, Wolynes P. Erratum to ‘Nature and nurture in protein folding and binding’ [Curr Opin Struct Biol 2010, 20:1–2] Current Opinion in Structural Biology. 20: 397. DOI: 10.1016/J.Sbi.2010.03.003 |
0.374 |
|
2010 |
Craig PO, Lätzer J, Weinkam P, Hoffman R, Komives E, Wolynes P. Prediction of H Exchange from Perfectly Funneled Structure Based Models Biophysical Journal. 98: 638a. DOI: 10.1016/J.Bpj.2009.12.3493 |
0.833 |
|
2010 |
Hoffman RM, Craig PO, DeVries IL, Komives EA, Wolynes PG. Folding Kinetics of IkB: Excursions Through the Energy Landscape Biophysical Journal. 98: 200a. DOI: 10.1016/J.Bpj.2009.12.1067 |
0.462 |
|
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 |
0.656 |
|
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 |
0.598 |
|
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 |
0.632 |
|
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 |
0.832 |
|
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 |
0.394 |
|
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 |
0.823 |
|
2009 |
Wolynes PG. Spatiotemporal structures in aging and rejuvenating glasses. Proceedings of the National Academy of Sciences of the United States of America. 106: 1353-8. PMID 19188612 DOI: 10.1073/Pnas.0812418106 |
0.311 |
|
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 |
0.812 |
|
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 |
0.661 |
|
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 |
0.326 |
|
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 |
0.801 |
|
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 |
0.579 |
|
2008 |
Stevenson JD, Wolynes PG. On the surface of glasses. The Journal of Chemical Physics. 129: 234514. PMID 19102545 DOI: 10.1063/1.3041651 |
0.655 |
|
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 |
0.795 |
|
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 |
0.659 |
|
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 |
0.724 |
|
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 |
0.33 |
|
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 |
0.732 |
|
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 |
0.648 |
|
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 |
0.744 |
|
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 |
0.799 |
|
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 |
0.833 |
|
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 |
0.817 |
|
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 |
0.576 |
|
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 |
0.796 |
|
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 |
0.712 |
|
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 |
0.424 |
|
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 |
0.653 |
|
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 |
0.653 |
|
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 |
0.59 |
|
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 |
0.787 |
|
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 |
0.569 |
|
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 |
0.753 |
|
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 |
0.666 |
|
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 |
0.596 |
|
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 |
0.752 |
|
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 |
0.791 |
|
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 |
0.595 |
|
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 |
0.602 |
|
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 |
0.611 |
|
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 |
0.592 |
|
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 |
0.444 |
|
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 |
0.734 |
|
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 |
0.617 |
|
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 |
0.628 |
|
2006 |
Lubchenko V, Silbey RJ, Wolynes PG. Electrodynamics of amorphous media at low temperatures Molecular Physics. 104: 1325-1335. DOI: 10.1080/00268970500395661 |
0.67 |
|
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 |
0.657 |
|
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 |
0.777 |
|
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 |
0.58 |
|
2005 |
Wolynes PG. Recent successes of the energy landscape theory of protein folding and function. Quarterly Reviews of Biophysics. 38: 405-10. PMID 16934172 DOI: 10.1017/S0033583505004075 |
0.423 |
|
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 |
0.664 |
|
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 |
0.709 |
|
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 |
0.734 |
|
2005 |
Oliveberg M, Wolynes PG. The experimental survey of protein-folding energy landscapes. Quarterly Reviews of Biophysics. 38: 245-88. PMID 16780604 DOI: 10.1017/S0033583506004185 |
0.44 |
|
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 |
0.641 |
|
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 |
0.33 |
|
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 |
0.507 |
|
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 |
0.796 |
|
2005 |
Bhattacharyya SM, Bagchi B, Wolynes PG. Bridging the gap between the mode coupling and the random first order transition theories of structural relaxation in liquids. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 031509. PMID 16241446 DOI: 10.1103/Physreve.72.031509 |
0.328 |
|
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 |
0.67 |
|
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 |
0.659 |
|
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 |
0.826 |
|
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 |
0.423 |
|
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 |
0.73 |
|
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 |
0.713 |
|
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 |
0.463 |
|
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 |
0.314 |
|
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 |
0.683 |
|
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 |
0.679 |
|
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 |
0.551 |
|
2004 |
Wolynes PG. Latest folding game results: protein A barely frustrates computationalists. Proceedings of the National Academy of Sciences of the United States of America. 101: 6837-8. PMID 15123824 DOI: 10.1073/Pnas.0402034101 |
0.487 |
|
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 |
0.625 |
|
2004 |
Gruebele M, Wolynes PG. Vibrational energy flow and chemical reactions. Accounts of Chemical Research. 37: 261-7. PMID 15096063 DOI: 10.1021/Ar030230T |
0.338 |
|
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 |
0.754 |
|
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 |
0.68 |
|
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 |
0.591 |
|
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 |
0.749 |
|
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 |
0.641 |
|
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 |
0.706 |
|
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 |
0.738 |
|
2003 |
Hall RW, Wolynes PG. Microscopic theory of network glasses. Physical Review Letters. 90: 085505. PMID 12633439 DOI: 10.1103/Physrevlett.90.085505 |
0.522 |
|
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 |
0.7 |
|
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 |
0.67 |
|
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 |
0.809 |
|
2003 |
Hall RW, Wolynes PG. Hall and Wolynes Reply: Physical Review Letters. 91. DOI: 10.1103/Physrevlett.91.159602 |
0.479 |
|
2003 |
Westfahl H, Schmalian J, Wolynes PG. Dynamical mean-field theory of quantum stripe glasses Physical Review B. 68. DOI: 10.1103/Physrevb.68.134203 |
0.306 |
|
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 |
0.675 |
|
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 |
0.766 |
|
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 |
0.607 |
|
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 |
0.819 |
|
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 |
0.742 |
|
2002 |
McCammon J, Wolynes PG. Enlarging the landscape Current Opinion in Structural Biology. 12: 143-145. DOI: 10.1016/S0959-440X(02)00301-9 |
0.399 |
|
2002 |
Wu S, Westfahl H, Schmalian J, Wolynes PG. Theory of microemulsion glasses Chemical Physics Letters. 359: 1-7. DOI: 10.1016/S0009-2614(02)00246-4 |
0.319 |
|
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 |
0.659 |
|
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 |
0.486 |
|
2001 |
Eastwood MP, Hardin C, Luthey-Schulten Z, Wolynes PG. Evaluating protein structure-prediction schemes using energy landscape theory Ibm Journal of Research and Development. 45: 475-497. DOI: 10.1147/Rd.453.0475 |
0.636 |
|
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 |
0.746 |
|
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 |
0.762 |
|
2001 |
Eastwood MP, Wolynes PG. Role of explicitly cooperative interactions in protein folding funnels: A simulation study The Journal of Chemical Physics. 114: 4702. DOI: 10.1063/1.1315994 |
0.429 |
|
2001 |
Xia X, Wolynes PG. Diffusion and the Mesoscopic Hydrodynamics of Supercooled Liquids† The Journal of Physical Chemistry B. 105: 6570-6573. DOI: 10.1021/Jp004616M |
0.332 |
|
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 |
0.754 |
|
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 |
0.809 |
|
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 |
0.526 |
|
2000 |
Leitner D, Wolynes P. Heat flow through an insulating nanocrystal Physical Review E. 61: 2902-2908. DOI: 10.1103/Physreve.61.2902 |
0.548 |
|
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 |
0.745 |
|
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 |
0.753 |
|
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 |
0.576 |
|
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 |
0.78 |
|
1999 |
Wolynes PG, Eaton WA. The physics of protein folding Physics World. 12: 39-44. DOI: 10.1088/2058-7058/12/9/24 |
0.351 |
|
1999 |
Takada S, Luthey-Schulten Z, Wolynes PG. Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer The Journal of Chemical Physics. 110: 11616-11629. DOI: 10.1063/1.479101 |
0.645 |
|
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 |
0.691 |
|
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 |
0.71 |
|
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 |
0.543 |
|
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 |
0.477 |
|
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 |
0.597 |
|
1998 |
Gruebele M, Wolynes PG. Satisfying turns in folding transitions. Nature Structural Biology. 5: 662-5. PMID 9699621 DOI: 10.1038/1354 |
0.357 |
|
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 |
0.618 |
|
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 |
0.677 |
|
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 |
0.763 |
|
1998 |
Plotkin SS, Wolynes PG. Non-Markovian Configurational Diffusion and Reaction Coordinates for Protein Folding Physical Review Letters. 80: 5015-5018. DOI: 10.1103/Physrevlett.80.5015 |
0.393 |
|
1998 |
Wolynes P. The concept of nucleation Folding and Design. 3: R107. DOI: 10.1016/S1359-0278(98)00055-8 |
0.4 |
|
1997 |
Wolynes PG. Entropy Crises in Glasses and Random Heteropolymers. Journal of Research of the National Institute of Standards and Technology. 102: 187-194. PMID 27805136 DOI: 10.6028/Jres.102.014 |
0.315 |
|
1997 |
Wolynes PG. As simple as can be? Nature Structural Biology. 4: 871-4. PMID 9360595 DOI: 10.1038/Nsb1197-871 |
0.332 |
|
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 |
0.745 |
|
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 |
0.748 |
|
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 |
0.719 |
|
1997 |
Wolynes PG. Folding funnels and energy landscapes of larger proteins within the capillarity approximation. Proceedings of the National Academy of Sciences of the United States of America. 94: 6170-5. PMID 9177189 DOI: 10.1073/Pnas.94.12.6170 |
0.48 |
|
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 |
0.625 |
|
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 |
0.697 |
|
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 |
0.749 |
|
1997 |
Leitner DM, Wolynes PG. Quantization of the Stochastic Pump Model of Arnold Diffusion Physical Review Letters. 79: 55-58. DOI: 10.1103/Physrevlett.79.55 |
0.555 |
|
1997 |
Takada S, Wolynes PG. Microscopic theory of critical folding nuclei and reconfiguration activation barriers in folding proteins The Journal of Chemical Physics. 107: 9585-9598. DOI: 10.1063/1.475256 |
0.424 |
|
1997 |
Plotkin SS, Wang J, Wolynes PG. Statistical mechanics of a correlated energy landscape model for protein folding funnels The Journal of Chemical Physics. 106: 2932-2948. DOI: 10.1063/1.473355 |
0.456 |
|
1997 |
Wang J, Plotkin SS, Wolynes PG. Configurational Diffusion on a Locally Connected Correlated
Energy Landscape; Application to Finite,
Random Heteropolymers Journal De Physique I. 7: 395-421. DOI: 10.1051/Jp1:1997168 |
0.363 |
|
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 |
0.722 |
|
1997 |
Leitner DM, Wolynes PG. Vibrational Mixing and Energy Flow in Polyatomics: Quantitative Prediction Using Local Random Matrix Theory The Journal of Physical Chemistry A. 101: 541-548. DOI: 10.1021/Jp9619088 |
0.612 |
|
1997 |
Saven JG, Wolynes PG. Local signals in the energy landscape of collapsed helical proteins Physica D: Nonlinear Phenomena. 107: 330-337. DOI: 10.1016/S0167-2789(97)00102-4 |
0.429 |
|
1997 |
Plotkin SS, Wang J, Wolynes PG. Statistical mechanis of correlated energy landscape models for random heteropolymers and proteins Physica D: Nonlinear Phenomena. 107: 322-325. DOI: 10.1016/S0167-2789(97)00100-0 |
0.427 |
|
1997 |
Panchenko AR, Luthey-Schulten Z, Wolynes PG. Foldons as independently folding units of proteins Physica D: Nonlinear Phenomena. 107: 312-315. DOI: 10.1016/S0167-2789(97)00098-5 |
0.761 |
|
1997 |
Leitner DM, Wolynes PG. Quantum energy flow during molecular isomerization Chemical Physics Letters. 280: 411-418. DOI: 10.1016/S0009-2614(97)01120-2 |
0.587 |
|
1997 |
Leitner DM, Wolynes PG. Intramolecular energy flow in the condensed phase: effects of dephasing on localization in the quantum stochastic pump model Chemical Physics Letters. 276: 289-295. DOI: 10.1016/S0009-2614(97)00859-2 |
0.583 |
|
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 |
0.577 |
|
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 |
0.314 |
|
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 |
0.726 |
|
1996 |
Wolynes PG. Symmetry and the energy landscapes of biomolecules. Proceedings of the National Academy of Sciences of the United States of America. 93: 14249-55. PMID 8962034 DOI: 10.1073/Pnas.93.25.14249 |
0.418 |
|
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 |
0.73 |
|
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 |
0.623 |
|
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 |
0.758 |
|
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 |
0.759 |
|
1996 |
Leitner DM, Wolynes PG. Vibrational relaxation and energy localization in polyatomics: Effects of high‐order resonances on flow rates and the quantum ergodicity transition The Journal of Chemical Physics. 105: 11226-11236. DOI: 10.1063/1.472920 |
0.573 |
|
1996 |
Wang J, Saven JG, Wolynes PG. Kinetics In A Globally Connected, Correlated Random Energy Model Journal of Chemical Physics. 105: 11276-11284. DOI: 10.1063/1.472869 |
0.749 |
|
1996 |
Schofield SA, Wyatt RE, Wolynes PG. Computational study of many‐dimensional quantum vibrational energy redistribution. I. Statistics of the survival probability The Journal of Chemical Physics. 105: 940-952. DOI: 10.1063/1.471937 |
0.335 |
|
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 |
0.568 |
|
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. DOI: 10.1063/1.470943 |
0.643 |
|
1996 |
Wang J, Wolynes P. Instantons and the Fluctuating Path Description of Reactions in Complex Environments The Journal of Physical Chemistry. 100: 1129-1136. DOI: 10.1021/Jp951325I |
0.307 |
|
1996 |
Zheng C, Makarov V, Wolynes PG. Statistical Survey of Transition States and Conformational Substates of the Sperm Whale Myoglobin−CO Reaction System Journal of the American Chemical Society. 118: 2818-2824. DOI: 10.1021/Ja9523092 |
0.437 |
|
1996 |
Leitner DM, Wolynes PG. Statistical properties of localized vibrational eigenstates Chemical Physics Letters. 258: 18-24. DOI: 10.1016/0009-2614(96)00614-8 |
0.565 |
|
1996 |
Wang J, Saven JG, Wolynes PG. Kinetics in a globally connected, correlated random energy model Journal of Chemical Physics. 105: 11276-11284. |
0.698 |
|
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. |
0.581 |
|
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 |
0.487 |
|
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 |
0.63 |
|
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 |
0.748 |
|
1995 |
Wolynes PG. Biomolecular folding in vacuo!!!(?) Proceedings of the National Academy of Sciences of the United States of America. 92: 2426-7. PMID 7708658 DOI: 10.1073/Pnas.92.7.2426 |
0.443 |
|
1995 |
Panchenko AR, Wang J, Nienhaus GU, Wolynes PG. Analysis of Ligand Binding to Heme Proteins Using a Fluctuating Path Description The Journal of Physical Chemistry. 99: 9278-9282. DOI: 10.1021/J100022A049 |
0.607 |
|
1995 |
Schofield SA, Wolynes PG. Rate Theory and Quantum Energy Flow in Molecules: Modeling the Effects of Anisotropic Diffusion and of Dephasing The Journal of Physical Chemistry. 99: 2753-2763. DOI: 10.1021/J100009A034 |
0.334 |
|
1995 |
Luthey-Schulten Z, Ramirez BE, Wolynes PG. Helix-Coil, Liquid Crystal, and Spin Glass Transitions of a Collapsed Heteropolymer The Journal of Physical Chemistry. 99: 2177-2185. DOI: 10.1021/J100007A057 |
0.617 |
|
1994 |
Gulukota K, Wolynes PG. Statistical mechanics of kinetic proofreading in protein folding in vivo. Proceedings of the National Academy of Sciences of the United States of America. 91: 9292-6. PMID 7937758 DOI: 10.1073/Pnas.91.20.9292 |
0.455 |
|
1994 |
Saven JG, Wang J, Wolynes PG. Kinetics of protein folding: The dynamics of globally connected rough energy landscapes with biases Journal of Chemical Physics. 101: 11037-11043. DOI: 10.1063/1.467855 |
0.769 |
|
1994 |
Schofield SA, Wolynes PG. Rate theory and non-RRKM quantum dynamics described by local random matrix models Chemical Physics Letters. 217: 497-502. DOI: 10.1016/0009-2614(93)E1439-N |
0.337 |
|
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. |
0.742 |
|
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 |
0.683 |
|
1993 |
Gentile AC, Schofield SA, Wolynes PG. Non‐Rice–Ramsperger–Kassel–Marcus dynamics and the statistics of reaction rates in chaotic systems The Journal of Chemical Physics. 98: 7898-7902. DOI: 10.1063/1.464545 |
0.31 |
|
1993 |
Schofield SA, Wolynes PG. A scaling perspective on quantum energy flow in molecules The Journal of Chemical Physics. 98: 1123-1131. DOI: 10.1063/1.464337 |
0.33 |
|
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 |
0.545 |
|
1993 |
Wong CF, Zheng C, Shen J, McCammon JA, Wolynes PG. Cytochrome c: a molecular proving ground for computer simulations The Journal of Physical Chemistry. 97: 3100-3110. DOI: 10.1021/J100115A008 |
0.422 |
|
1992 |
Bohr HG, Wolynes PG. Initial events of protein folding from an information-processing viewpoint. Physical Review. A. 46: 5242-5248. PMID 9908746 DOI: 10.1103/Physreva.46.5242 |
0.37 |
|
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 |
0.68 |
|
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 |
0.708 |
|
1992 |
IRWIN J, BOHR H, MOCHIZUKI K, WOLYNES P. CLASSIFICATION AND PREDICTION OF PROTEIN SIDE-CHAINS BY NEURAL NETWORK TECHNIQUES International Journal of Neural Systems. 3: 177-182. DOI: 10.1142/S0129065792000504 |
0.352 |
|
1992 |
Tanimura Y, Wolynes PG. The interplay of tunneling, resonance, and dissipation in quantum barrier crossing: A numerical study The Journal of Chemical Physics. 96: 8485-8496. DOI: 10.1063/1.462301 |
0.489 |
|
1992 |
Wade RC, Bohr H, Wolynes PG. Prediction of water binding sites on proteins by neural networks Journal of the American Chemical Society. 114: 8284-8285. DOI: 10.1021/Ja00047A046 |
0.306 |
|
1991 |
Tanimura Y, Wolynes PG. Quantum and classical Fokker-Planck equations for a Gaussian-Markovian noise bath. Physical Review. A. 43: 4131-4142. PMID 9905511 DOI: 10.1103/Physreva.43.4131 |
0.459 |
|
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 |
0.583 |
|
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 |
0.422 |
|
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 |
0.481 |
|
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 |
0.338 |
|
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 |
0.386 |
|
1990 |
Bryngelson JD, Wolynes PG. A simple statistical field theory of heteropolymer collapse with application to protein folding Biopolymers. 30: 177-188. DOI: 10.1002/Bip.360300117 |
0.4 |
|
1989 |
Bryngelson JD, Wolynes PG. Intermediates and barrier crossing in a random energy model (with applications to protein folding) The Journal of Physical Chemistry. 93: 6902-6915. DOI: 10.1021/J100356A007 |
0.34 |
|
1988 |
Zheng C, Wong CF, McCammon JA, Wolynes PG. Quantum simulation of ferrocytochrome c. Nature. 334: 726-8. PMID 2842687 DOI: 10.1038/334726A0 |
0.475 |
|
1988 |
Ohmine I, Tanaka H, Wolynes PG. Large local energy fluctuations in water. II. Cooperative motions and fluctuations The Journal of Chemical Physics. 89: 5852-5860. DOI: 10.1063/1.455536 |
0.355 |
|
1988 |
Mccammon JA, Harvey SC, Wolynes PG. Dynamics of Proteins and Nucleic Acids Physics Today. 41: 105-106. DOI: 10.1063/1.2811564 |
0.392 |
|
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 |
0.5 |
|
1987 |
Bryngelson JD, Wolynes PG. Spin glasses and the statistical mechanics of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 84: 7524-8. PMID 3478708 DOI: 10.1073/Pnas.84.21.7524 |
0.405 |
|
1987 |
Kirkpatrick TR, Wolynes PG. Connections between some kinetic and equilibrium theories of the glass transition Physical Review A. 35: 3072-3080. DOI: 10.1103/Physreva.35.3072 |
0.314 |
|
1987 |
Wolynes PG. Linearized microscopic theories of nonequilibrium solvation The Journal of Chemical Physics. 86: 5133-5136. DOI: 10.1063/1.452632 |
0.339 |
|
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 |
0.549 |
|
1987 |
Cline RE, Wolynes PG. Stochastic dynamic models of curve crossing phenomena in condensed phases The Journal of Chemical Physics. 86: 3836-3844. DOI: 10.1063/1.451942 |
0.317 |
|
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 |
0.525 |
|
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 |
0.333 |
|
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 |
0.57 |
|
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 |
0.368 |
|
1985 |
Behrman EC, Wolynes PG. Dynamics of a two‐level system coupled to a dissipative bath: Comparisons of analytical theories with Monte Carlo simulation The Journal of Chemical Physics. 83: 5863-5869. DOI: 10.1063/1.449861 |
0.334 |
|
1985 |
Behrman EC, Jongeward GA, Wolynes PG. An optimized random phase approximation for the dynamics of tunneling systems in condensed phases The Journal of Chemical Physics. 83: 668-673. DOI: 10.1063/1.449535 |
0.305 |
|
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 |
0.483 |
|
1985 |
Wahlstrand KJ, Wolynes PG. Simulation of a relativistic soliton model of crystalline polymer dynamics The Journal of Chemical Physics. 82: 5259-5263. DOI: 10.1063/1.448649 |
0.316 |
|
1983 |
Calef DF, Wolynes PG. Classical solvent dynamics and electron transfer. II. Molecular aspects The Journal of Chemical Physics. 78: 470-482. DOI: 10.1063/1.444472 |
0.309 |
|
1982 |
Chandler D, Schweizer KS, Wolynes PG. Electronic States of a Topologically Disordered System: Exact Solution of the Mean Spherical Model for Liquids Physical Review Letters. 49: 1100-1103. DOI: 10.1103/Physrevlett.49.1100 |
0.438 |
|
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 |
0.47 |
|
1981 |
Hynes JT, Wolynes PG. A continuum theory for quadrupole relaxation of ions in solution The Journal of Chemical Physics. 75: 395-401. DOI: 10.1063/1.441796 |
0.492 |
|
1981 |
Chandler D, Wolynes PG. Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids The Journal of Chemical Physics. 74: 4078-4095. DOI: 10.1063/1.441588 |
0.496 |
|
1980 |
Berne BJ, Skinner JL, Wolynes PG. Impulsive stochastic models of molecular relaxation and isomerization reactions The Journal of Chemical Physics. 73: 4314-4320. DOI: 10.1063/1.440713 |
0.679 |
|
1980 |
Skinner JL, Wolynes PG. Solitons, defect diffusion, and dielectric relaxation of polymers The Journal of Chemical Physics. 73: 4022-4025. DOI: 10.1063/1.440630 |
0.61 |
|
1980 |
Skinner JL, Wolynes PG. Transition state and Brownian motion theories of solitons The Journal of Chemical Physics. 73: 4015-4021. DOI: 10.1063/1.440629 |
0.631 |
|
1980 |
Skinner JL, Wolynes PG. General kinetic models of activated processes in condensed phases The Journal of Chemical Physics. 72: 4913-4927. DOI: 10.1063/1.439776 |
0.622 |
|
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 |
0.523 |
|
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 |
0.583 |
|
1978 |
Skinner JL, Wolynes PG. Relaxation processes and chemical kinetics The Journal of Chemical Physics. 69: 2143-2150. DOI: 10.1063/1.436814 |
0.595 |
|
1978 |
Schulten K, Wolynes PG. Semiclassical description of electron spin motion in radicals including the effect of electron hopping The Journal of Chemical Physics. 68: 3292-3297. DOI: 10.1063/1.436135 |
0.315 |
|
1977 |
Wolynes PG, Deutch JM. Dynamical orientation correlations in solution The Journal of Chemical Physics. 67: 733-741. DOI: 10.1063/1.434881 |
0.544 |
|
1977 |
Montgomery JA, Berne BJ, Wolynes PG, Deutch JM. On the effects of translation–rotation coupling on hydrodynamic diffusion tensors The Journal of Chemical Physics. 67: 5971-5972. DOI: 10.1063/1.434773 |
0.569 |
|
1977 |
McCammon JA, Wolynes PG. Nonsteady hydrodynamics of biopolymer motions The Journal of Chemical Physics. 66: 1452-1456. DOI: 10.1063/1.434107 |
0.44 |
|
1976 |
Wolynes PG, Deutch JM. Hydrodynamic boundary conditions and polymer dynamics The Journal of Chemical Physics. 65: 2030-2031. DOI: 10.1063/1.433259 |
0.508 |
|
1976 |
Wolynes PG, Deutch JM. Slip boundary conditions and the hydrodynamic effect on diffusion controlled reactions The Journal of Chemical Physics. 65: 450-454. DOI: 10.1063/1.432788 |
0.531 |
|
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