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。Markov State Models Provide Insights into Dynamic Modulation of Protein Function
Diwakar Shukla et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
Folding Propensity of Anoplin: A Molecular Dynamics Study of the Native Peptide and Four Mutated Isoforms
Massimiliano Aschi et al.
BIOPOLYMERS (2015)
Folding Thermodynamics and Mechanism of Five Trp-Cage Variants from Replica-Exchange MD Simulations with RSFF2 Force Field
Chen-Yang Zhou et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes
Ana Elisa Bergues-Pupo et al.
NUCLEIC ACIDS RESEARCH (2015)
G-quadruplexes and their regulatory roles in biology
Daniela Rhodes et al.
NUCLEIC ACIDS RESEARCH (2015)
Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations
Petr Stadlbauer et al.
BIOCHIMIE (2014)
Kinetics of Two Slow Conformational Transitions of the Quadruplex Structure of the Thrombin Binding Aptamer and their Potassium Dependence
Harikrushan Ranpura et al.
BIOPHYSICAL JOURNAL (2014)
Unfolding and Conformational Variations of ThrombinBinding DNA Aptamers: Synthesis, Circular Dichroism and Molecular Dynamics Simulations
Lidan Sun et al.
CHEMMEDCHEM (2014)
Ligand induced change of β2 adrenergic receptor from active to inactive conformation and its implication for the closed/open state of the water channel: insight from molecular dynamics simulation, free energy calculation and Markov state model analysis
Qifeng Bai et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2014)
A straightforward modification in the thrombin binding aptamer improving the stability, affinity to thrombin and nuclease resistance
Veronica Esposito et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2014)
Stability and bioactivity of thrombin binding aptamers modified with D-/L-isothymidine in the loop regions
Baobin Cai et al.
ORGANIC & BIOMOLECULAR CHEMISTRY (2014)
Comparison of the 'Chemical' and 'Structural' Approaches to the Optimization of the Thrombin-Binding Aptamer
Olga Tatarinova et al.
PLOS ONE (2014)
Millisecond dynamics of RNA polymerase II translocation at atomic resolution
Daniel-Adriano Silva et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
A regular thymine tetrad and a peculiar supramolecular assembly in the first crystal structure of an all-LNA G-quadruplex
Irene Russo Krauss et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2014)
The G-Triplex DNA
Vittorio Limongelli et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2013)
Dynamics of an Intrinsically Disordered Protein Reveal Metastable Conformations That Potentially Seed Aggregation
Qin Qiao et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)
Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations
Petr Stadlbauer et al.
NUCLEIC ACIDS RESEARCH (2013)
A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase
Lin-Tai Da et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
DNA aptamer functionalized nanomaterials for intracellular analysis, cancer cell imaging and drug delivery
Hang Xing et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2012)
Free-Energy Landscape of a Thrombin-Binding DNA Aptamer in Aqueous Environment
Eunae Kim et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II
Lin-Tai Da et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Energetic Basis of Human Telomeric DNA Folding into G-Quadruplex Structures
Matjaz Boncina et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity
Irene Russo Krauss et al.
NUCLEIC ACIDS RESEARCH (2012)
Multiple stepwise pattern for potential of mean force in unfolding the thrombin binding aptamer in complex with Sr2+
Changwon Yang 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)
Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events
Weinan E et al.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 61 (2010)
Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-Scale Explicit Solvent Simulations
Roman Reshetnikov et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
Folding Pathways of Human Telomeric Type-1 and Type-2 G-Quadruplex Structures
Tomoko Mashimo et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)
Vincent A. Voelz et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Molecular dynamics simulation of SRP GTPases: Towards an understanding of the complex formation from equilibrium fluctuations
Mingjun Yang et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
The structures of quadruplex nucleic acids and their drug complexes
Stephen Neidle
CURRENT OPINION IN STRUCTURAL BIOLOGY (2009)
Structure-activity relationships of a caged thrombin binding DNA aptamer: Insight gained from molecular dynamics simulation studies
Prabha Jayapal et al.
JOURNAL OF STRUCTURAL BIOLOGY (2009)
Using generalized ensemble simulations and Markov state models to identify conformational states
Gregory R. Bowman et al.
METHODS (2009)
Mechanisms contributing to synaptic Ca2+ signals and their heterogeneity in hair cells
Thomas Frank et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Targeting telomeres and telomerase
Anne De Cian et al.
BIOCHIMIE (2008)
In vivo veritas:: Using yeast to probe the biological functions of G-quadruplexes
Jay E. Johnson et al.
BIOCHIMIE (2008)
Transition networks for modeling the kinetics of conformational change in macromolecules
Frank Noe et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2008)
Refinenement of the AMBER force field for nucleic acids:: Improving the description of α/γ conformers
Alberto Perez et al.
BIOPHYSICAL JOURNAL (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)
Hierarchical analysis of conformational dynamics in biomolecules:: Transition networks of metastable states
Frank Noe et al.
JOURNAL OF CHEMICAL PHYSICS (2007)
NMR study of the folding-unfolding mechanism for the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG)
X Mao et al.
BIOPHYSICAL CHEMISTRY (2005)
NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+
XA Mao et al.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2004)
Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates
R Stefl et al.
BIOPHYSICAL JOURNAL (2003)
G-quadruplex DNA structures - Variations on a theme
T Simonsson
BIOLOGICAL CHEMISTRY (2001)
Structures of the potassium-saturated, 2:1, and intermediate, 1:1,forms of a quadruplex DNA
VM Marathias et al.
NUCLEIC ACIDS RESEARCH (2000)