Peter G Wolynes

发表

Stochastic resonances in a distributed genetic broadcasting system: the NFκB/IκB paradigm

Zhipeng Wang, Davit A Potoyan, Peter G Wolynes, 2019, Journal of The Royal Society Interface.

Surveying biomolecular frustration at atomic resolution

Cecilia Clementi, Peter G Wolynes, Xun Chen, 2020, Nature Communications.

Protein Structure Refinement Guided by Atomic Packing Frustration Analysis.

Peter G Wolynes, Mingchen Chen, Xun Chen, 2020, The journal of physical chemistry. B.

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

Peter G Wolynes, Mingchen Chen, Xingcheng Lin, 2016, The journal of physical chemistry. B.

Theory, simulations, and experiments show that proteins fold by multiple pathways

Peter G Wolynes, William A Eaton, P. Wolynes, 2017, Proceedings of the National Academy of Sciences.

Frustration in biomolecules

Peter G Wolynes, Elizabeth A Komives, Diego U Ferreiro, 2013, Quarterly Reviews of Biophysics.

Simulation studies of the fidelity of biomolecular structure ensemble recreation.

Peter G Wolynes, Michael P Eastwood, Joachim Lätzer, 2006, The Journal of chemical physics.

Stochastic dynamics of genetic broadcasting networks

Davit A Potoyan, Peter G Wolynes, Davit A. Potoyan, 2016, bioRxiv.

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

Peter G Wolynes, Wei Lu, Mingchen Chen, 2018, Journal of chemical theory and computation.

Dichotomous noise models of gene switches.

Davit A Potoyan, Peter G Wolynes, Davit A. Potoyan, 2015, The Journal of chemical physics.

Stochastic gene expression as a many-body problem

Peter G Wolynes, Masaki Sasai, P. Wolynes, 2003, Proceedings of the National Academy of Sciences of the United States of America.

A variational approach to the stochastic aspects of cellular signal transduction.

Peter G Wolynes, Yueheng Lan, Garegin A Papoian, 2006, The Journal of chemical physics.

Protein Structure Prediction: The Next Generation.

Peter G Wolynes, Chenghang Zong, Michael P Eastwood, 2006, Journal of chemical theory and computation.

Protein Structure Prediction in CASP13 using AWSEM-Suite.

Wei Lu, Xun Chen, Peter G Wolynes, 2020, Journal of chemical theory and computation.

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

Juan J de Pablo, Peter G Wolynes, Xun Chen, 2021, PLoS Comput. Biol..

FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations

Peter G Wolynes, Diego U Ferreiro, Leandro G Radusky, 2021, Bioinform..

Molecular stripping in the NF-κB/IκB/DNA genetic regulatory network

Davit A Potoyan, Peter G Wolynes, Elizabeth A Komives, 2015, Proceedings of the National Academy of Sciences.

Water Mediated Interactions and the Protein Folding Phase Diagram in the Temperature-Pressure Plane.

Peter G Wolynes, Nicholas P Schafer, Nicholas P. Schafer, 2015, The journal of physical chemistry. B.

On the spontaneous collective motion of active matter

Peter G Wolynes, P. Wolynes, Shenshen Wang, 2011, Proceedings of the National Academy of Sciences.

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

Wei Lu, Peter G Wolynes, Mingchen Chen, 2017, The journal of physical chemistry. B.

Transferable model for chromosome architecture

Peter G Wolynes, Erez Lieberman Aiden, José N Onuchic, 2016, Proceedings of the National Academy of Sciences.

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

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2005, Journal of molecular biology.

Predictive energy landscapes for folding α-helical transmembrane proteins

Peter G Wolynes, Nicholas P Schafer, Nicholas P. Schafer, 2014, Proceedings of the National Academy of Sciences.

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

Osamu Miyashita, Peter G Wolynes, José N Onuchic, 2005, The journal of physical chemistry. B.

Localizing Frustration in Proteins Using All-Atom Energy Functions.

Cecilia Clementi, Peter G Wolynes, Nicholas P Schafer, 2019, The journal of physical chemistry. B.

Local frustration around enzyme active sites

Peter G Wolynes, Diego U Ferreiro, Maria I Freiberger, 2019, Proceedings of the National Academy of Sciences.

Electrostatics, structure prediction, and the energy landscapes for protein folding and binding

Peter G Wolynes, Nicholas P Schafer, Weihua Zheng, 2016, Protein science : a publication of the Protein Society.

Theory of aging in structural glasses.

Peter G Wolynes, Vassiliy Lubchenko, 2004, The Journal of chemical physics.

Genomic Energy Landscapes.

Peter G Wolynes, Bin Zhang, P. Wolynes, 2017, Biophysical journal.

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

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2005, Physical biology.

Frustration, function and folding.

Peter G Wolynes, Elizabeth A Komives, Diego U Ferreiro, 2017, Current opinion in structural biology.

Nonequilibrium statistical mechanical models for cytoskeletal assembly: towards understanding tensegrity in cells.

Peter G Wolynes, Tongye Shen, P. Wolynes, 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

On the dephasing of genetic oscillators

Davit A Potoyan, Peter G Wolynes, Davit A. Potoyan, 2013, Proceedings of the National Academy of Sciences.

Protein structure prediction using basin-hopping.

Peter G Wolynes, David J Wales, Michael C Prentiss, 2008, The Journal of chemical physics.

Tensegrity and motor-driven effective interactions in a model cytoskeleton.

Peter G Wolynes, P. Wolynes, Shenshen Wang, 2012, The Journal of chemical physics.

Protein topology determines binding mechanism.

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2004, Proceedings of the National Academy of Sciences of the United States of America.

P versus Q: structural reaction coordinates capture protein folding on smooth landscapes.

Peter G Wolynes, Yaakov Levy, Samuel S. Cho, 2006, Proceedings of the National Academy of Sciences of the United States of America.

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

Peter G Wolynes, Nicholas P Schafer, Faruck Morcos, 2014, Proceedings of the National Academy of Sciences.

Aggregation landscapes of Huntingtin exon 1 protein fragments and the critical repeat length for the onset of Huntington’s disease

Peter G Wolynes, Mingchen Chen, P. Wolynes, 2017, Proceedings of the National Academy of Sciences.

Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles

Peter G Wolynes, Harry B Gray, Jay R Winkler, 2009, Proceedings of the National Academy of Sciences.

Chemical frustration in the protein folding landscape: grand canonical ensemble simulations of cytochrome c.

Peter G Wolynes, Floyd E Romesberg, P. Wolynes, 2009, Biochemistry.

Latest folding game results: protein A barely frustrates computationalists.

Peter G Wolynes, P. Wolynes, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Facilitation, complexity growth, mode coupling, and activated dynamics in supercooled liquids

Peter G Wolynes, Biman Bagchi, P. Wolynes, 2008, Proceedings of the National Academy of Sciences.

The spectrum of biomolecular states and motions

Peter G Wolynes, P. Wolynes, Joseph A Hegler, 2008, HFSP journal.

Localizing frustration in native proteins and protein assemblies

Peter G Wolynes, Elizabeth A Komives, Diego U Ferreiro, 2007, Proceedings of the National Academy of Sciences.

Theory of structural glasses and supercooled liquids.

Peter G Wolynes, P. Wolynes, V. Lubchenko, 2007, Annual review of physical chemistry.

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

Peter G Wolynes, Tongye Shen, Yaakov Levy, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Exploring the Free Energy Landscape of Nucleosomes.

Peter G Wolynes, Bin Zhang, Weihua Zheng, 2016, Journal of the American Chemical Society.

Consequences of localized frustration for the folding mechanism of the IM7 protein

Peter G Wolynes, Diego U Ferreiro, Ludovico Sutto, 2007, Proceedings of the National Academy of Sciences.

Origins of barriers and barrierless folding in BBL

Peter G Wolynes, Samuel S. Cho, Samuel S Cho, 2008, Proceedings of the National Academy of Sciences.

Predictive energy landscapes for folding membrane protein assemblies.

Peter G Wolynes, Nicholas P Schafer, Nicholas P. Schafer, 2015, The Journal of chemical physics.

Variationally determined free energy profiles for structural models of proteins: characteristic temperatures for folding and trapping.

Peter G Wolynes, Tongye Shen, Chenghang Zong, 2008, The journal of physical chemistry. B.

Funneling and frustration in the energy landscapes of some designed and simplified proteins.

Peter G Wolynes, Nicholas P Schafer, Nicholas P. Schafer, 2013, The Journal of chemical physics.

Free energy landscapes for initiation and branching of protein aggregation

Peter G Wolynes, Nicholas P Schafer, Weihua Zheng, 2013, Proceedings of the National Academy of Sciences.

Scanning malleable transition state ensembles: comparing theory and experiment for folding protein U1A.

Peter G Wolynes, Tongye Shen, P. Wolynes, 2005, Biochemistry.

The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations.

Peter G Wolynes, Amedeo Caflisch, Yaakov Levy, 2004, Journal of molecular biology.

Optimizing physical energy functions for protein folding

Shoji Takada, Peter G Wolynes, Yoshimi Fujitsuka, 2003, Proteins.

The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family.

Peter G Wolynes, Elizabeth A Komives, Diego U Ferreiro, 2005, Journal of molecular biology.

The folding energy landscape and free energy excitations of cytochrome c.

Peter G Wolynes, Floyd E Romesberg, P. Wolynes, 2010, Accounts of chemical research.

Stabilizing IkappaBalpha by "consensus" design.

Peter G Wolynes, Elizabeth A Komives, Diego U Ferreiro, 2007, Journal of molecular biology.

Influence of decoys on the noise and dynamics of gene expression.

Peter G Wolynes, Aleksandra M Walczak, P. Wolynes, 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

Bridging the gap between the mode coupling and the random first order transition theories of structural relaxation in liquids.

Peter G Wolynes, Biman Bagchi, Sarika Maitra Bhattacharyya, 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

Intermolecular forces and the glass transition.

Peter G Wolynes, Randall W Hall, 2008, The journal of physical chemistry. B.

Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

Peter G Wolynes, Yaakov Levy, Samuel S. Cho, 2009, Proceedings of the National Academy of Sciences.

Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of alpha/beta proteins.

Peter G Wolynes, Chenghang Zong, Johan Ulander, 2006, Journal of the American Chemical Society.

The ultimate fate of supercooled liquids.

Peter G Wolynes, Jacob D Stevenson, P. Wolynes, 2010, The journal of physical chemistry. A.

Protein structure prediction: do hydrogen bonding and water-mediated interactions suffice?

Peter G Wolynes, Chenghang Zong, Garegin A Papoian, 2010, Methods.

Capillarity theory for the fly-casting mechanism

Peter G Wolynes, Emmanuel Trizac, Yaakov Levy, 2010, Proceedings of the National Academy of Sciences.

Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes.

Peter G Wolynes, Elizabeth A Komives, Diego U Ferreiro, 2011, Journal of the American Chemical Society.

Characterization of alkaline transitions in ferricytochrome c using carbon-deuterium infrared probes.

Peter G Wolynes, Shigeo Matsuda, Floyd E Romesberg, 2008, Biochemistry.

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

Peter G Wolynes, Yaakov Levy, José N Onuchic, 2007, Journal of the American Chemical Society.

The capillarity picture and the kinetics of one-dimensional protein folding

Peter G Wolynes, Diego U Ferreiro, P. Wolynes, 2008, Proceedings of the National Academy of Sciences.

The Aggregation Free Energy Landscapes of Polyglutamine Repeats.

Peter G Wolynes, Mingchen Chen, Weihua Zheng, 2016, Journal of the American Chemical Society.

Role of water mediated interactions in protein-protein recognition landscapes.

Peter G Wolynes, Johan Ulander, Garegin A Papoian, 2003, Journal of the American Chemical Society.

Energy landscapes of a mechanical prion and their implications for the molecular mechanism of long-term memory

Peter G Wolynes, Mingchen Chen, Weihua Zheng, 2016, Proceedings of the National Academy of Sciences.

Evolution, energy landscapes and the paradoxes of protein folding.

Peter G Wolynes, P. Wolynes, 2015, Biochimie.