Protein Folding Theory: From Lattice to All-Atom Models

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Construction of Energy Functions for Lattice Heteropolymer Models: Efficient Encodings for Constraint Satisfaction Programming and Quantum Annealing

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Experimental Characterization of the Folding Kinetics of the Notch Ankyrin Domain

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Unfolded state of peptides

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The folding pathway of ubiquitin from all-atom molecular dynamics simulations

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Solution of Levinthal’s Paradox and a Physical Theory of Protein Folding Times

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The rate dependent response of a bistable chain at finite temperature

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Using deeply trapped intermediates to map the cytochrome c folding landscape

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Mechanism of Helix Nucleation and Propagation: Microscopic View from Microsecond Time Scale MD Simulations

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Class‐specific correlations between protein folding rate, structure‐derived, and sequence‐derived descriptors

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From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization

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Reversible Thermal Denaturation of a 60-kDa Genetically Engineered β-Sheet Polypeptide

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Descriptor‐based protein remote homology identification

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Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: The energy landscape analysis of a hot spot at the intermolecular interface

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Unfolding a molecular trefoil derived from a zwitterionic metallopeptide to form self-assembled nanostructures

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Interaction of an ionic complementary peptide with a hydrophobic graphite surface

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What Determines Protein Folding Type? An Investigation of Intrinsic Structural Properties and its Implications for Understanding Folding Mechanisms

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Calculation of Mutational Free Energy Changes in Transition States for Protein Folding

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Self-assembly of peptides into a β-barrel motif

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Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?

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Critical nucleation size in the folding of small apparently two‐state proteins

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A Framework for Describing Topological Frustration in Models of Protein Folding

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Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model

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As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy

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Hydrophobicity Scaling of Aqueous Interfaces by an Electrostatic Mapping

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Molecular mechanism for the effects of trehalose on β-hairpin folding revealed by molecular dynamics simulation

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Sampling Kinetic Protein Folding Pathways using All-Atom Models

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A Directed Essential Dynamics Simulation of Peptide Folding

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Analysing the origin of long-range interactions in proteins using lattice models

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Thermodynamics and folding landscapes of large proteins from a statistical mechanical model

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The Folding Pathway of α-Lactalbumin Elucidated by the Technique of Disulfide Scrambling

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Non‐native interactions, effective contact order, and protein folding: A mutational investigation with the energetically frustrated hydrophobic model

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Modeling ensembles of transmembrane β‐barrel proteins

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Membrane protein native state discrimination by implicit membrane models

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Effects of Topology and Excluded Volume on Protein Denatured State Conformational Properties

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The Cytochrome c Folding Landscape Revealed by Electron-transfer Kinetics

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How long does it take to equilibrate the unfolded state of a protein?

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Force-Induced Unfolding Simulations of the Human Notch1 Negative Regulatory Region: Possible Roles of the Heterodimerization Domain in Mechanosensing

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Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains

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The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing

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Computational studies of protein folding

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Dynamics of hierarchical folding on energy landscapes of hexapeptides

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Molecular simulation of protein dynamics in nanopores. II. Diffusion

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A Structure-Centric View of Protein Evolution, Design, and Adaptation

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Classification of common functional loops of kinase super‐families

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Adsorption of an Ionic Complementary Peptide on the Hydrophobic Graphite Surface

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In silico profiling of tyrosine kinases binding specificity and drug resistance using Monte Carlo simulations with the ensembles of protein kinase crystal structures

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Thermodynamical properties of simple models of protein‐like heteropolymers

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Molecular Dynamics Simulation of Peptide Folding

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Equilibrium Distribution of Mutators in the Single Fitness Peak Model

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Alteration of the disulfide‐coupled folding pathway of BPTI by circular permutation

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Confinement in nanopores can destabilize α-helix folding proteins and stabilize the β structures

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All-atom Monte Carlo Simulation of GCAA RNA Folding

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Protein translocation through a tunnel induces changes in folding kinetics: A lattice model study

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A multi-population memetic algorithm for the 3-D protein structure prediction problem

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Dominant Reaction Pathways by Quantum Computing

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Barriers and dynamical paths in alternating Gibbs sampling of restricted Boltzmann machines

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Temperature‐dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface

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Squeezed exponential kinetics to describe a nonglassy downhill folding as observed in a lattice protein model

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Prediction of Protein Folding Rates from Structural Topology and Complex Network Properties

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Imprints of function on the folding landscape: functional role for an intermediate in a conserved eukaryotic binding protein

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The Physics of the Interactions Governing Folding and Association of Proteins

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Computational proteomics of biomolecular interactions in the sequence and structure space of the tyrosine kinome: Deciphering the molecular basis of the kinase inhibitors selectivity

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Folding kinetics of a polymer

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Initial Disulfide Formation Steps in the Folding of an ω-Conotoxin

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The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways

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Folding of Top7 in unbiased all‐atom Monte Carlo simulations

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Protein Folding Simulations: Combining Coarse-grained Models and All-atom Molecular Dynamics

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Differentiation between two‐state and multi‐state folding proteins based on sequence

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Integrating computer-based de novo drug design and multidimensional filtering for desirable drugs

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A survey of methionine-aromatic interaction geometries in the oxidoreductase class of enzymes: What could Met-aromatic interactions be doing near metal sites?

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Improvement of Structure-Based Potentials for Protein Folding by Native and Nonnative Hydrogen Bonds

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Correlation between evolutionary structural development and protein folding

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Thermal unfolding simulations of a multimeric protein—Transition state and unfolding pathways

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Using Secondary Structure Information for Protein Folding in CLP( )

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Sequence dependence of polymer dynamics in quenched disordered media: Weak attraction facilitates transport

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Hydrophobe-Water Interactions: Methane as a Model

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Cyclic Peptides

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Properties of Grafted Amphiphilic Chains. A Computer Simulation Study

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Progressing from folding trajectories to transition state ensemble in proteins

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Peptide adsorption on the hydrophobic surface: A free energy perspective

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How Good Are Simplified Models for Protein Structure Prediction?

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Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins

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Structure and dynamics of the ‘protein folding code’ inferred using Tlusty's topological rate distortion approach

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Effects of frustration, confinement, and surface interactions on the dimerization of an off-lattice β-barrel protein

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CoC: a database of universally conserved residues in protein folds

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Molecular Dynamics Simulations to Study Protein Folding and Unfolding

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Evolving model of amino acid networks

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Refinement of the long‐range order parameter in predicting folding rates of two‐state proteins

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Role of supersecondary structural elements in protein G folding

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Insight into protein topology from Monte Carlo simulations

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Computational models of molecular self-organization in cellular environments

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Geometric and physical considerations for realistic protein models

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On the Relationship Between Protein Stability and Folding Kinetics: A Comparative Study of the N-terminal Domains of RNase HI, E. coli and Bacillus stearothermophilus L9

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Combinatorial vector fields and the valley structure of fitness landscapes

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Levinthal’s Paradox Revisited, and Dismissed

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Identifying the protein folding nucleus using molecular dynamics

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Theoretical studies of protein-folding thermodynamics and kinetics

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Nucleation mechanisms in protein folding

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