Peter G. Wolynes

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Will Computer Design Become a Matter of Evolution

Peter G. Wolynes, 1992 .

The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures

Aleksandra M. Walczak, Peter G. Wolynes, Diego U. Ferreiro, 2008, PLoS Comput. Biol..

Folding funnels: The key to robust protein structure prediction

Zaida Luthey-Schulten, Peter G. Wolynes, Michael P. Eastwood, 2002, J. Comput. Chem..

Topology, structure and energy landscape of human chromosomes

Peter G. Wolynes, Bin Zhang, 2015 .

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

Peter G. Wolynes, David J. Wales, Michael C. Prentiss, 2010, PLoS Comput. Biol..

Protein frustratometer: a tool to localize energetic frustration in protein molecules

Adrian Gustavo Turjanski, Peter G. Wolynes, R. Gonzalo Parra, 2012, Nucleic Acids Res..

PCCP--a society journal going from strength to strength.

Ruth Nussinov, David Parker, Peter G. Wolynes, 2015, Physical chemistry chemical physics : PCCP.

A Bayesian approach to sequence alignment algorithms for protein structure recognition

Zaida Luthey-Schulten, Richard A. Goldstein, Peter G. Wolynes, 1994, 1994 Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences.

1 Scientific interview

Peter G. Wolynes, Thomas A. Witten, Jorge Kurchan, 2011 .

Evaluating protein structure-prediction schemes using energy landscape theory

Zaida Luthey-Schulten, Peter G. Wolynes, Michael P. Eastwood, 2001, IBM J. Res. Dev..

Stochastic dynamics of genetic broadcasting networks.

Peter G. Wolynes, Davit A. Potoyan, 2017 .

Molecular-replacement phasing using predicted protein structures from AWSEM-Suite

Xun Chen, Mingchen Chen, Peter G. Wolynes, 2020, IUCrJ.

Classification and Prediction of Protein Side-Chains by Neural Network Techniques

Peter G. Wolynes, Henrik G. Bohr, J. Irwin, 1992, Int. J. Neural Syst..

Book review:Functional integration: Theory and applications

Peter G. Wolynes, 1982 .

Deciding fate in adverse times: Sporulation and competence in Bacillus subtilis

Peter G. Wolynes, José N. Onuchic, Daniel Schultz, 2009, Proceedings of the National Academy of Sciences.

The AWSEM-Amylometer: predicting amyloid propensity and fibril topology using an optimized folding landscape model

Mingchen Chen, Peter G. Wolynes, Weihua Zheng, 2017, bioRxiv.

Multiscale modeling of three-dimensional genome

Peter G. Wolynes, Bin Zhang, 2016 .

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics

Peter G. Wolynes, R. Gonzalo Parra, Leandro G. Radusky, 2016, Nucleic Acids Res..

THE STATISTICAL MECHANICAL BASIS OF SEQUENCE ALIGNMENT ALGORITHMS FOR PROTEIN STRUCTURE RECOGNITION

Richard A. Goldstein, Peter G. Wolynes, Zaida Ann Luthey-Schulten, 1996 .

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

Xun Chen, Mingchen Chen, Peter G. Wolynes, 2020, bioRxiv.

Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach

Peter G. Wolynes, Zaida Ann Luthey-Schulten, Michael P. Eastwood, 2002 .

Protein Structure Refinement Guided by Atomic Packing Frustration Analysis

Wei Lu, Mingchen Chen, Peter G. Wolynes, 2020, bioRxiv.

The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome

Peter G. Wolynes, José N. Onuchic, Vinícius G. Contessoto, 2019, bioRxiv.

φ-Value Analysis of Apo-Azurin Folding: Comparison between Experiment and Theory†

Tongye Shen, Chenghang Zong, Peter G. Wolynes, 2006 .

A universal origin for secondary relaxations in supercooled liquids and structural glasses

Peter G. Wolynes, Jacob D. Stevenson, P. Wolynes, 2009, Nature Physics.

Variational Theory for Site Resolved Protein Folding Free Energy Surfaces

Shoji Takada, John J. Portman, Peter G. Wolynes, 1998, cond-mat/9805366.

Large local energy fluctuations in water. II. Cooperative motions and fluctuations

Peter G. Wolynes, Hideki Tanaka, P. Wolynes, 1988 .

Protein structure prediction: making AWSEM AWSEM‐ER by adding evolutionary restraints

Peter G. Wolynes, Nicholas P. Schafer, P. Wolynes, 2017, Proteins.

Energy landscape underlying spontaneous insertion and folding of an alpha-helical transmembrane protein into a bilayer

Wei Lu, Peter G. Wolynes, Nicholas P. Schafer, 2018, Nature Communications.

Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics

Shoji Takada, John J. Portman, Peter G. Wolynes, 2000, cond-mat/0008455.

Glassy Dynamics of Random Heteropolymers

Shoji Takada, Peter G. Wolynes, 1997 .

Helix-Coil, Liquid Crystal, and Spin Glass Transitions of a Collapsed Heteropolymer

Zaida Luthey-Schulten, Peter G. Wolynes, Benjamin E. Ramirez, 1995 .

Frustration in the energy landscapes of multidomain protein misfolding

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

Dynamical orientation correlations in solution

Peter G. Wolynes, John M. Deutch, P. Wolynes, 1977 .

The Folding Landscapes of Metalloproteins

Peter G. Wolynes, P. Wolynes, Patrick Weinkam, 2010 .

Dynamical mean-field theory of quantum stripe glasses

Peter G. Wolynes, Harry Westfahl, Jörg Schmalian, 2003 .

Classical solvent dynamics and electron transfer. 1. Continuum theory

Peter G. Wolynes, P. Wolynes, Daniel F. Calef, 1983 .

Cooperative Conformational Transitions in Phenylene Ethynylene Oligomers: Chain-Length Dependence

Jeffery G. Saven, Peter G. Wolynes, P. Wolynes, 1999 .

A second molecular biology revolution? The energy landscapes of biomolecular function.

Ruth Nussinov, Peter G. Wolynes, R. Nussinov, 2014, Physical chemistry chemical physics : PCCP.

Discrete Kinetic Models from Funneled Energy Landscape Simulations

Peter G. Wolynes, Elizabeth A. Komives, Nicholas P. Schafer, 2012, PloS one.

Hydrodynamic boundary conditions and mode-mode coupling theory

Peter G. Wolynes, P. Wolynes, 1976 .

Role of Topology, Nonadditivity, and Water-Mediated Interactions in Predicting the Structures of α/β Proteins

Chenghang Zong, Johan Ulander, Peter G. Wolynes, 2006 .

STATISTICAL MECHANICS OF THE COMBINATORIAL SYNTHESIS AND ANALYSIS OF FOLDING MACROMOLECULES

Jeffery G. Saven, Peter G. Wolynes, P. Wolynes, 1997 .

Entropy Crises in Glasses and Random Heteropolymers

Peter G. Wolynes, P. Wolynes, 1997, Journal of research of the National Institute of Standards and Technology.

Molecular stripping in the $NF\kappa B/I\kappa B/DNA$ genetic regulatory network

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

The shapes of cooperatively rearranging regions in glass-forming liquids

Peter G. Wolynes, Jacob D. Stevenson, Joerg Schmalian, 2006 .

Exploring the aggregation free energy landscape of the amyloid-β protein (1–40)

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

Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions

Peter G. Wolynes, José N. Onuchic, J. Onuchic, 1999 .

Prediction of water binding sites on proteins by neural networks

Rebecca C. Wade, Henrik Bohr, Peter G. Wolynes, 1992 .

Protein Structure Prediction Using an Associated Memory Hamiltonian and All-Atom Molecular Dynamics Simulations

Peter G. Wolynes, P. Wolynes, K. Kwac, 2008 .

Molecular stripping, targets and decoys as modulators of oscillations in the NF-κB/IκBα/DNA genetic network

Zhipeng Wang, Peter G. Wolynes, Davit A. Potoyan, 2016, Journal of The Royal Society Interface.

Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution

J. Andrew McCammon, Peter G. Wolynes, P. Wolynes, 1998 .

Enlarging the landscape

J. Andrew McCammon, Peter G. Wolynes, 2002 .

Statistical mechanics of a cat's cradle

Tongye Shen, Peter G. Wolynes, 2006 .

Chemical physics of protein folding

Peter G. Wolynes, Alan R. Fersht, William A. Eaton, 1998, Proceedings of the National Academy of Sciences.

A simple statistical field theory of heteropolymer collapse with application to protein folding

Peter G. Wolynes, Joseph D. Bryngelson, P. Wolynes, 1990 .

A Monte Carlo approach for the real time dynamics of tunneling systems in condensed phases

Elizabeth C. Behrman, Peter G. Wolynes, Gary A. Jongeward, 1983 .

Braiding topology and the energy landscape of chromosome organization proteins

Peter G. Wolynes, José N. Onuchic, Aram Davtyan, 2019, Proceedings of the National Academy of Sciences.

Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach

Shoji Takada, John J. Portman, Peter G. Wolynes, 2000, cond-mat/0008454.

Role of explicitly cooperative interactions in protein folding funnels: A simulation study

Peter G. Wolynes, Michael P. Eastwood, P. Wolynes, 2001 .

Energy Landscape Analysis of Protein Dimers

Peter G. Wolynes, José N. Onuchic, Yaakov Levy, 2004 .

AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes

Wei Lu, Xun Chen, Mingchen Chen, 2020, Nucleic Acids Res..

The aperiodic crystal picture and free energy barriers in glasses

Peter G. Wolynes, Randall W. Hall, R. W. Hall, 1987 .

Biomolecules: Where the Physics of Complexity and Simplicity Meet

Peter G. Wolynes, Hans Frauenfelder, P. Wolynes, 1994 .

Quantum simulations of conformation reorganization in the electron transfer reactions of tuna cytochrome c

J. Andrew McCammon, Peter G. Wolynes, P. Wolynes, 1991 .

As simple as can be?

Peter G. Wolynes, P. Wolynes, 1997, Nature Structural Biology.

Spin Glass Ideas and the Protein Folding Problems

Peter G. Wolynes, P. Wolynes, 1992 .

Dynamics of a two-level system coupled to a dissipative bath: Comparisons of analytical theories with Monte Carlo simulation

Elizabeth C. Behrman, Peter G. Wolynes, P. Wolynes, 1985 .

Stabilizing IκBα by “Consensus” Design

Peter G. Wolynes, Diego U. Ferreiro, Elizabeth A. Komives, 2007 .

Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids

Peter G. Wolynes, David Chandler, P. Wolynes, 1981 .

NMR relaxation parameters in molecules with internal motion: exact Langevin trajectory results compared with simplified relaxation models

Ronald M. Levy, Peter G. Wolynes, Martin Karplus, 1981 .

Some quantum weirdness in physiology

Peter G. Wolynes, P. Wolynes, 2009, Proceedings of the National Academy of Sciences.

Slip boundary conditions and the hydrodynamic effect on diffusion controlled reactions

Peter G. Wolynes, John M. Deutch, P. Wolynes, 1976 .

Quantum simulation of ferrocytochrome c

J. Andrew McCammon, Peter G. Wolynes, P. Wolynes, 1988, Nature.

General kinetic models of activated processes in condensed phases

Peter G. Wolynes, P. Wolynes, J. Skinner, 1980 .

Water in protein structure prediction - eScholarship

Johan Ulander, Peter G. Wolynes, Zaida Ann Luthey-Schulten, 2004 .

Kinetics of protein folding: The dynamics of globally connected rough energy landscapes with biases

Jeffery G. Saven, Peter G. Wolynes, P. Wolynes, 1994 .

Coupling the folding of homologous proteins

J. Andrew McCammon, Peter G. Wolynes, 1998 .

Phenotypic variability of growing cellular populations

Jeff Hasty, Tongye Shen, Peter G. Wolynes, 2007, Proceedings of the National Academy of Sciences.

Molecular dynamics of associative memory hamiltonians for protein tertiary structure recognition

Peter G. Wolynes, Mark S. Friedrichs, P. Wolynes, 1990 .

New methods of structure refinement for macromolecular structure determination by NMR

Peter G. Wolynes, 1998 .

Forging tools for refining predicted protein structures

Wei Lu, Xun Chen, Mingchen Chen, 2019, Proceedings of the National Academy of Sciences.