Relation between Free Energy Landscapes of Proteins and Dynamics

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Principal Component Analysis

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The Energy Landscapes and Motions of Proteins

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Generalized Cumulant Expansion Method

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Generalized-ensemble algorithms for molecular simulations of biopolymers

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Principal Component Analysis for Protein Folding Dynamics

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Transition networks for modeling the kinetics of conformational change in macromolecules

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Energy landscape of a small peptide revealed by dihedral angle principal component analysis

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Systemic administration of an antagonist of the ATP-sensitive receptor P2X7 improves recovery after spinal cord injury

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First-Principles Calculation of the Folding Free Energy of a Three-Helix Bundle Protein

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Hidden complexity of free energy surfaces for peptide (protein) folding

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A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data

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Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures

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Dihedral angle principal component analysis of molecular dynamics simulations

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Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

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Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

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Interpreting the folding kinetics of helical proteins

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Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

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Structural analysis of WW domains and design of a WW prototype.

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Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

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Preorganized secondary structure as an important determinant of fast protein folding.

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Modification and Optimization of the United-Residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins

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Taking a Walk on a Landscape

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Molecular Dynamics with the United-Residue Model of Polypeptide Chains. II. Langevin and Berendsen-Bath Dynamics and Tests on Model α-Helical Systems

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Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation

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Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin

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Prediction of protein conformation on the basis of a search for compact structures: Test on avian pancreatic polypeptide

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Testing protein-folding simulations by experiment: B domain of protein A

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Molecular Dynamics with the United-Residue Model of Polypeptide Chains. I. Lagrange Equations of Motion and Tests of Numerical Stability in the Microcanonical Mode

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The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: Lessons for protein design?

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Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains

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Absence of a stable intermediate on the folding pathway of protein A

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Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide

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Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems

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How Complex Is the Dynamics of Peptide Folding?

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Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

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Dynamics of one-state downhill protein folding

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All-Atom Ab Initio Folding of a Diverse Set of Proteins

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A structure-based method for derivation of all-atom potentials for protein folding

Kussell, E. L., Shimada, J., & Shakhnovich, E. I. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.072665799 · Cited by 78

Microsecond folding dynamics of the F13W G29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump

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Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain

Karanicolas, J., & Brooks, C. L. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0304825101 · Cited by 69

How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics?

Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2009) · Physical Review Letters · doi:10.1103/physrevlett.102.238102 · Cited by 52

High-resolution protein folding with a transferable potential

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Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model 1 1Edited by A. R. Fersht

Berriz, G. F., & Shakhnovich, E. I. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4792 · Cited by 48

An Improved Functional Form for the Temperature Scaling Factors of the Components of the Mesoscopic UNRES Force Field for Simulations of Protein Structure and Dynamics

Shen, H., Liwo, A., & Scheraga, H. A. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp901788q · Cited by 48

The protein folding problem: global optimization of force fields

H., A. S. (2004) · Frontiers in bioscience · doi:10.2741/1482 · Cited by 35

Revealing Free Energy Landscape From MD Data via Conditional Angle Partition Tree

Jiang, H., Li, H., Wong, W. H., & Fan, X. (2023) · IEEE/ACM Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2022.3172352 · Cited by 4