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。Exploring the Folding Free Energy Landscape of Insulin Using Bias Exchange Metadynamics
Nevena Todorova et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2009)
Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations
Vanessa Leone et al.
PLOS COMPUTATIONAL BIOLOGY (2009)
Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water
Jarek Juraszek et al.
BIOPHYSICAL JOURNAL (2008)
Bluegene/L applications:: Parallelism on a massive scale
Bronis R. De Supinski et al.
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS (2008)
Predicting the effect of a point mutation on a protein fold: The villin and advillin headpieces and their Pro62Ala mutants
Stefano Piana et al.
JOURNAL OF MOLECULAR BIOLOGY (2008)
Coarse master equations for peptide folding dynamics
Nicolae-Viorel Buchete et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
Alessandro Laio et al.
REPORTS ON PROGRESS IN PHYSICS (2008)
The Trp-cage: optimizing the stability of a globular miniprotein
Bipasha Barua et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2008)
Identification of Biomolecular conformations from incomplete torsion angle observations by hidden Markov models
Alexander Fischer et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)
Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study
Cesar Augusto F. De Oliveira et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
Calculation of the Free Energy and Cooperativity of Protein Folding
Alex Kentsis et al.
PLOS ONE (2007)
A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein
K. Hun Mok et al.
NATURE (2007)
A bias-exchange approach to protein folding
Stefano Piana et al.
JOURNAL OF PHYSICAL CHEMISTRY B (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)
Unfolding thermodynamics of Trp-cage, a 20 residue miniprotein, studied by differential scanning calorimetry and circular dichroism spectroscopy
Werner W. Streicher et al.
BIOCHEMISTRY (2007)
Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent:: On the structure and possible role of internal water
Dietmar Paschek et al.
JOURNAL OF STRUCTURAL BIOLOGY (2007)
Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study
Juergen Graf et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Complex network analysis of free-energy landscapes
D. Gfeller et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations
David A. C. Beck et al.
JOURNAL OF STRUCTURAL BIOLOGY (2007)
Comparison of multiple amber force fields and development of improved protein backbone parameters
Viktor Hornak et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)
Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
J. Juraszek et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics
Giovanni Bussi et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Early events in protein folding explored by rapid mixing methods
Heinrich Roder et al.
CHEMICAL REVIEWS (2006)
Using massively parallel simulation and Markovian models to study protein folding: Examining the dynamics of the villin headpiece
G Jayachandran et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Equilibrium free energies from nonequilibrium metadynamics
G Bussi et al.
PHYSICAL REVIEW LETTERS (2006)
Ultrafast folding of a computationally designed Trp-cage mutant:: Trp2-cage
MR Bunagan et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2006)
Automated model reduction for complex systems exhibiting metastability
Illia Horenko et al.
MULTISCALE MODELING & SIMULATION (2006)
A microscopic view of miniprotein folding: Enhanced folding efficiency through formation of an intermediate
H Neuweiler et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
UV-resonance Raman thermal unfolding study of Trp-cage shows that it is not a simple two-state miniprotein
Z Ahmed et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2005)
Energy landscape paving simulations of the trp-cage protein
A Schug et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
Finite temperature string method for the study of rare events
E Weinan et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2005)
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
G Hummer
NEW JOURNAL OF PHYSICS (2005)
Reconstructing the density of states by history-dependent metadynamics
C Micheletti et al.
PHYSICAL REVIEW LETTERS (2004)
Simulations of the role of water in the protein-folding mechanism
YM Rhee et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Phylogeny of protein-folding trajectories reveals a unique pathway to native structure
M Ota et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Computing time scales from reaction coordinates by milestoning
AK Faradjian et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
Y Duan et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Trp-cage: Folding free energy landscape in explicit water
RH Zhou
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Transition-path sampling of β-hairpin folding
PG Bolhuis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Reproducible protein folding with the stochastic tunneling method
A Schug et al.
PHYSICAL REVIEW LETTERS (2003)
Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
B Zagrovic et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
Understanding folding and design: Replica-exchange simulations of Trp-cage fly miniproteins
JW Pitera et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments
YG Mu et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2003)
A novel path sampling method for the calculation of rate constants
TS van Erp et al.
JOURNAL OF CHEMICAL PHYSICS (2003)
Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution
S Chowdhury et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
The Trp cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
CD Snow et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)
Smaller and faster:: The 20-residue Trp-cage protein folds in 4 μs
LL Qiu et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)
All-atom structure prediction and folding simulations of a stable protein
C Simmerling et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2002)
Dihedral angles of tripeptides in solution directly determined by polarized Raman and FTIR spectroscopy
R Schweitzer-Stenner
BIOPHYSICAL JOURNAL (2002)
Designing a 20-residue protein
JW Neidigh et al.
NATURE STRUCTURAL BIOLOGY (2002)
Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models
MY Shen et al.
BIOPHYSICAL JOURNAL (2002)
An efficient algorithm for large-scale detection of protein families
AJ Enright et al.
NUCLEIC ACIDS RESEARCH (2002)
Dihedral angles of trialanine in D2O determined by combining FTIR and polarized visible Raman spectroscopy
R Schweitzer-Stenner et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2001)
GROMACS 3.0: a package for molecular simulation and trajectory analysis
E Lindahl et al.
JOURNAL OF MOLECULAR MODELING (2001)
Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy
S Woutersen et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2000)
分享论文
