Physicochemical bases for protein folding, dynamics, and protein-ligand binding

154 Protein folding and binding funnels: a common driving force and a common mechanism

(2013) Yue-Hui Xie et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

153 Wonderful roles of the entropy in protein dynamics, binding and folding

(2013) Yue-Hui Xie et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

The free energy landscape of protein folding and dynamics: a global view

(2013) Li-Quan Yang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms

(2013) Li-Quan Yang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

(2013) D. Granata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Stoichiometry Driven Universal Spatial Organization of Backbones of Folded Proteins: Are there Chargaff's Rules for Protein Folding?

(2012) Aditya Mittal et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Insight Derived from Molecular Dynamics Simulation into Substrate-Induced Changes in Protein Motions of Proteinase K

(2012) Yan Tao et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Thermal Stability and Unfolding Pathways of Sso7d and its Mutant F31A: Insight from Molecular Dynamics Simulation

(2012) Xianjin Xu et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Is Stoichiometry-Driven Protein Folding Getting Out of Thermodynamic Control?

(2012) Xing-Lai Ji et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Levinthal’s question revisited, and answered

(2012) Arieh Ben-Naim   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops

(2012) Y. D. Kwon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

(2012) W. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Implementing molecular dynamics on hybrid high performance computers – Particle–particle particle-mesh

(2011) W. Michael Brown et al.   COMPUTER PHYSICS COMMUNICATIONS

How, when and why proteins collapse: the relation to folding

(2011) Gilad Haran   CURRENT OPINION IN STRUCTURAL BIOLOGY

Effects of solvents on the intrinsic propensity of peptide backbone conformations

(2011) Wenfei Li et al.   PHYSICAL REVIEW E

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Dissection of the Zipping-and-Assembly Mechanism for Folding of Model Proteins

(2010) Sun Li et al.   CHINESE PHYSICS LETTERS

The effect of calciums on molecular motions of proteinase K

(2010) Shu-Qun Liu et al.   JOURNAL OF MOLECULAR MODELING

Nucleation process in the folding of a domain-swapped dimer

(2010) Zhiqiang Yan et al.   PHYSICAL REVIEW E

Protein folding dynamics: The diffusion-collision model and experimental data

(2010) Martin Karplus et al.   PROTEIN SCIENCE

Principles of protein folding - A perspective from simple exact models

(2010) Ken A. Dill et al.   PROTEIN SCIENCE

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K

(2009) Shu-Qun Liu et al.   JOURNAL OF MOLECULAR MODELING

Simulated annealing coupled replica exchange molecular dynamics—An efficient conformational sampling method

(2009) Srinivasaraghavan Kannan et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility

(2009) M. Pancera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Protein energy landscape roughness

(2008) Ruti Kapon et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Molecular motions of human HIV-1 gp120 envelope glycoproteins

(2008) Shu-Qun Liu et al.   JOURNAL OF MOLECULAR MODELING

How general is the nucleation-condensation mechanism?

(2008) Bengt Nölting et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS