相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign
Petra Kuehrova et al.
BIOPHYSICAL JOURNAL (2012)
Systematic Validation of Protein Force Fields against Experimental Data
Kresten Lindorff-Larsen et al.
PLOS ONE (2012)
Dynamics of protein folding: Probing the kinetic network of folding-unfolding transitions with experiment and theory
Ginka S. Buchner et al.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2011)
How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?
Stefano Piana et al.
BIOPHYSICAL JOURNAL (2011)
SHIFTX2: significantly improved protein chemical shift prediction
Beomsoo Han et al.
JOURNAL OF BIOMOLECULAR NMR (2011)
Markov state models based on milestoning
Christof Schuette et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
Markov models of molecular kinetics: Generation and validation
Jan-Hendrik Prinz et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale
Kyle A. Beauchamp et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein
Stefano Piana et al.
JOURNAL OF MOLECULAR BIOLOGY (2011)
The Free Energy Landscape Analysis of Protein (FIP35) Folding Dynamics
Sergei V. Krivov
JOURNAL OF PHYSICAL CHEMISTRY B (2011)
Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories
Thomas J. Lane et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables
Jan-Hendrik Prinz et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2011)
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments
Frank Noe et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments
Kyle A. Beauchamp et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Making connections between ultrafast protein folding kinetics and molecular dynamics simulations
Troy Cellmer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
How Fast-Folding Proteins Fold
Kresten Lindorff-Larsen et al.
SCIENCE (2011)
SPARTA plus : a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network
Yang Shen et al.
JOURNAL OF BIOMOLECULAR NMR (2010)
ON THE APPROXIMATION QUALITY OF MARKOV STATE MODELS
Marco Sarich et al.
MULTISCALE MODELING & SIMULATION (2010)
An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain
Andreas Reiner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw et al.
SCIENCE (2010)
Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding
Peter L. Freddolino et al.
BIOPHYSICAL JOURNAL (2009)
Progress and challenges in the automated construction of Markov state models for full protein systems
Gregory R. Bowman et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides
Robert B. Best et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Slow Transition between Two β-Strand Registers Is Dictated by Protein Unfolding
Matthew R. Evans et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Using generalized ensemble simulations and Markov state models to identify conformational states
Gregory R. Bowman et al.
METHODS (2009)
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
Frank Noe et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Probing invisible, low-populated states of protein molecules by relaxation dispersion NMR spectroscopy: An application to protein folding
Dmitry M. Korzhnev et al.
ACCOUNTS OF CHEMICAL RESEARCH (2008)
Are current molecular dynamics force fields too helical?
Robert B. Best et al.
BIOPHYSICAL JOURNAL (2008)
Transition networks for modeling the kinetics of conformational change in macromolecules
Frank Noe et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2008)
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
Berk Hess et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Fast procedure for reconstruction of full-atom protein models from reduced representations
Piotr Rotkiewicz et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)
Coarse master equations for peptide folding dynamics
Nicolae-Viorel Buchete et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Chemical, physical, and theoretical kinetics of an ultrafast folding protein
Jan Kubelka et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Heterogeneity even at the speed limit of folding: Large-scale molecular dynamics study of a fast-folding variant of the villin headpiece
Daniel L. Ensign et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Transient 2D IR spectroscopy of ubiquitin unfolding dynamics
Hoi Sung Chung et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
John D. Chodera et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Residue specific resolution of protein folding dynamics using isotope-edited infrared temperature jump spectroscopy
Scott H. Brewer et al.
BIOCHEMISTRY (2007)
A coarse graining method for the identification of transition rates between molecular conformations
Susanna Kube et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Structure-function-folding relationship in a WW domain
Marcus Jaeger et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Sub-microsecond protein folding
Jan Kubelka et al.
JOURNAL OF MOLECULAR BIOLOGY (2006)
High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein
TK Chiu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Reaction coordinates and rates from transition paths
RB Best et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Robust Perron cluster analysis in conformation dynamics
P Deuflhard et al.
LINEAR ALGEBRA AND ITS APPLICATIONS (2005)
Experimental tests of villin subdomain folding simulations
J Kubelka et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
Dynamic NMR line-shape analysis demonstrates that the villin headpiece subdomain folds on the microsecond time scale
MH Wang et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Rapid cooperative two-state folding of a miniature α-β protein and design of a thermostable variant
JC Horng et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
Medicine - The amyloid hypothesis of Alzheimer's disease: Progress and problems on the road to therapeutics
J Hardy et al.
SCIENCE (2002)
Coupling of folding and binding for unstructured proteins
HJ Dyson et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2002)
1H NMR study on the binding of Pin1 Trp-Trp domain with phosphothreonine peptides
R Wintjens et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2001)
Computer-based redesign of a protein folding pathway
S Nauli et al.
NATURE STRUCTURAL BIOLOGY (2001)
The ββα fold:: Explorations in sequence space
CA Sarisky et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains
P Deuflhard et al.
LINEAR ALGEBRA AND ITS APPLICATIONS (2000)