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。Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems
Shina C. L. Kamerlin et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 62 (2011)
Collapse kinetics and chevron plots from simulations of denaturant-dependent folding of globular proteins
Zhenxing Liu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
The Folding Energy Landscape and Free Energy Excitations of Cytochrome c
Patrick Weinkam et al.
ACCOUNTS OF CHEMICAL RESEARCH (2010)
Theoretical Perspectives on Protein Folding
D. Thirumalai et al.
ANNUAL REVIEW OF BIOPHYSICS, VOL 39 (2010)
Principles governing oligomer formation in amyloidogenic peptides
John E. Straub et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2010)
Models of macromolecular crowding effects and the need for quantitative comparisons with experiment
Adrian H. Elcock
CURRENT OPINION IN STRUCTURAL BIOLOGY (2010)
Transient Tertiary Structure Formation within the Ribosome Exit Port
Edward P. O'Brien et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Entropy as the driver of chromosome segregation
Suckjoon Jun et al.
NATURE REVIEWS MICROBIOLOGY (2010)
Chemically accurate coarse graining of double-stranded DNA
Alexey Savelyev et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor
Mitsunori Takano et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes
Anna Rychkova et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Promoter melting triggered by bacterial RNA polymerase occurs in three steps
Jie Chen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding
Apratim Dhar et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models
Benjamin M. Messer et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways
Paul C. Whitford et al.
RNA (2010)
Rigor to Post-Rigor Transition in Myosin V: Link between the Dynamics and the Supporting Architecture
Riina Tehver et al.
STRUCTURE (2010)
Metal Ion Dependence of Cooperative Collapse Transitions in RNA
Sarvin Moghaddam et al.
JOURNAL OF MOLECULAR BIOLOGY (2009)
Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases
Hanbin Liu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Refolding dynamics of stretched biopolymers upon force quench
Changbong Hyeon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Enzyme millisecond conformational dynamics do not catalyze the chemical step
Andrei V. Pisliakov et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Erez Lieberman-Aiden et al.
SCIENCE (2009)
Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
Huan-Xiang Zhou et al.
ANNUAL REVIEW OF BIOPHYSICS (2008)
Kinetic model for the coupling between allosteric transitions in GroEL and substrate protein folding and aggregation
Riina Tehver et al.
JOURNAL OF MOLECULAR BIOLOGY (2008)
Kinetics of loop formation in polymer chains
Ngo Minh Toan et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins
Changbong Hyeon et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2008)
Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes
Changbong Hyeon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model
Edward P. O'Brien et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations
Moritz Mickler et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Mechanical control of the directional stepping dynamics of the kinesin motor
Changbong Hyeon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
The MARTINI force field: Coarse grained model for biomolecular simulations
Siewert J. Marrink et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Charge density of divalent metal cations determines RNA stability
Eda Koculi et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Internal strain regulates the nucleotide binding site of the kinesin leading head
Changbong Hyeon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
Dynamics of allosteric transitions in GroEL
Changbong Hyeon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Determination of thermodynamics and kinetics of RNA reactions by force
Ignacio Tinoco et al.
QUARTERLY REVIEWS OF BIOPHYSICS (2006)
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
Changbong Hyeon et al.
STRUCTURE (2006)
Entropy-driven spatial organization of highly confined polymers: Lessons for the bacterial chromosome
Suckjoon Jun et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Molecular Simulations of cotranslational protein folding: Fragment stabilities, folding cooperativity, and trapping in the ribosome
Adrian H. Elcock
PLOS COMPUTATIONAL BIOLOGY (2006)
Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
Eugene Shakhnovich
CHEMICAL REVIEWS (2006)
Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase
N Koga et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Intrinsic rates and activation free energies from single-molecule pulling experiments
OK Dudko et al.
PHYSICAL REVIEW LETTERS (2006)
Kinetics of interior loop formation in semiflexible chains
C Hyeon et al.
JOURNAL OF CHEMICAL PHYSICS (2006)
Exploring the energy landscape of a small RNA hairpin
HR Ma et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)
Ribosome exit tunnel can entropically stabilize α-helices
G Ziv et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Scaling exponents and probability distributions of DNA end-to-end distance
F Valle et al.
PHYSICAL REVIEW LETTERS (2005)
Mechanical unfolding of RNA hairpins
C Hyeon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Cyclization of short DNA fragments and bending fluctuations of the double helix
Q Du et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Molecular crowding enhances native state stability and refolding rates of globular proteins
MS Cheung et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Extracting stacking interaction parameters for RNA from the data set of native structures
RI Dima et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
Force-clamp spectroscopy monitors the folding trajectory of a single protein
JM Fernandez et al.
SCIENCE (2004)
Theory of protein folding
JN Onuchic et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2004)
Spontaneous sharp bending of double-stranded DNA
TE Cloutier et al.
MOLECULAR CELL (2004)
Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase
M Strajbl et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Can energy landscape roughness of proteins and RNA be measured by using mechanical unfolding experiments?
CB Hyeon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Role of water mediated interactions in protein-protein recognition landscapes
GA Papoian et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Diffusion-limited loop formation of semiflexible polymers: Kramers theory and the intertwined time scales of chain relaxation and closing
S Jun et al.
EUROPHYSICS LETTERS (2003)
The origins of asymmetry in the folding transition states of protein L and protein G
J Karanicolas et al.
PROTEIN SCIENCE (2002)
Rapid compaction during RNA folding
R Russell et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
High resolution structure of the large ribosomal subunit from a mesophilic Eubacterium
J Harms et al.
CELL (2001)
The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
AP Minton
JOURNAL OF BIOLOGICAL CHEMISTRY (2001)
Chromosome territories, nuclear architecture and gene regulation in mammalian cells
T Cremer et al.
NATURE REVIEWS GENETICS (2001)
Topological and energetic factors: What determines the structural details of the transition state ensemble and en-route intermediates for protein folding? An investigation for small globular proteins
C Clementi et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
The way things move: Looking under the hood of molecular motor proteins
RD Vale et al.
SCIENCE (2000)
Dynamics of small loops in DNA molecules
AA Podtelezhnikov et al.
MACROMOLECULES (2000)
RNA folding energy landscapes
SJ Chen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)