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。Fluorescence-Detected Conformational Changes in Duplex DNA in Open Complex Formation by Escherichia coli RNA Polymerase: Upstream Wrapping and Downstream Bending Precede Clamp Opening and Insertion of the Downstream Duplex
Raashi Sreenivasan et al.
BIOCHEMISTRY (2020)
Stepwise Promoter Melting by Bacterial RNA Polymerase
James Chen et al.
MOLECULAR CELL (2020)
On the advantages of exploiting memory in Markov state models for biomolecular dynamics
Siqin Cao et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase
Mirjana Lilic et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference
Junhui Peng et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms
Abhishek Mazumder et al.
JOURNAL OF MOLECULAR BIOLOGY (2019)
Mechanisms of σ54-Dependent Transcription Initiation and Regulation
Amy E. Danson et al.
JOURNAL OF MOLECULAR BIOLOGY (2019)
The Core and Holoenzyme Forms of RNA Polymerase from Mycobacterium smegmatis
Tomas Kouba et al.
JOURNAL OF BACTERIOLOGY (2019)
Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding
Hande Boyaci et al.
NATURE (2019)
E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation
James Chen et al.
ELIFE (2019)
Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes
Diego Duchi et al.
NUCLEIC ACIDS RESEARCH (2018)
Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules
Wei Wang et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2018)
Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models
Ilona Christy Unarta et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)
The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp
Diego Duchi et al.
NUCLEIC ACIDS RESEARCH (2018)
Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts
Hande Boyaci et al.
ELIFE (2018)
Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
Nuria Plattner et al.
NATURE CHEMISTRY (2017)
RNA polymerase motions during promoter melting
Andrey Feklistov et al.
SCIENCE (2017)
Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA
Elizabeth A. Hubin et al.
ELIFE (2017)
Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity
Beibei Wang et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2017)
Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models
Lu Zhang et al.
ACCOUNTS OF CHEMICAL RESEARCH (2016)
Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit
Bin W. Zhang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2016)
Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue
Lin-Tai Da et al.
NATURE COMMUNICATIONS (2016)
Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations
Shoji Takada et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
Variational cross-validation of slow dynamical modes in molecular kinetics
Robert T. McGibbon et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein
Vadim Molodtsov et al.
JOURNAL OF MEDICINAL CHEMISTRY (2015)
A network of molecular switches controls the activation of the two-component response regulator NtrC
Dan K. Vanatta et al.
NATURE COMMUNICATIONS (2015)
Allostery through the computational microscope: cAMP activation of a canonical signalling domain
Robert D. Malmstrom et al.
NATURE COMMUNICATIONS (2015)
Cloud computing approaches for prediction of ligand binding poses and pathways
Morgan Lawrenz et al.
SCIENTIFIC REPORTS (2015)
Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement
Hanlun Jiang et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation
Lin-Tai Da et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Structure of a bacterial RNA polymerase holoenzyme open promoter complex
Brian Bae et al.
ELIFE (2015)
Initial Events in Bacterial Transcription Initiation
Emily F. Ruff et al.
BIOMOLECULES (2015)
Markov state models of biomolecular conformational dynamics
John D. Chodera et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)
Application of Molecular-Dynamics Based Markov State Models to Functional Proteins
Robert D. Malmstrom et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
Kai J. Kohlhoff et al.
NATURE CHEMISTRY (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)
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Sander Pronk et al.
BIOINFORMATICS (2013)
To milliseconds and beyond: challenges in the simulation of protein folding
Thomas J. Lane et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)
X-ray Crystal Structure of Escherichia coli RNA Polymerase σ70 Holoenzyme
Katsuhiko S. Murakami
JOURNAL OF BIOLOGICAL CHEMISTRY (2013)
Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis
Yusuke Naritomi et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Identification of slow molecular order parameters for Markov model construction
Guillermo Perez-Hernandez et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
Christian R. Schwantes et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Fuzzy spectral clustering by PCCA plus : application to Markov state models and data classification
Susanna Roeblitz et al.
ADVANCES IN DATA ANALYSIS AND CLASSIFICATION (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)
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
Adam Hospital et al.
BIOINFORMATICS (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)
Simple few-state models reveal hidden complexity in protein folding
Kyle A. Beauchamp et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Opening and Closing of the Bacterial RNA Polymerase Clamp
Anirban Chakraborty et al.
SCIENCE (2012)
Implementation of force distribution analysis for molecular dynamics simulations
Wolfram Stacklies et al.
BMC BIOINFORMATICS (2011)
Structural Basis for Promoter-10 Element Recognition by the Bacterial RNA Polymerase σ Subunit
Andrey Feklistov et al.
CELL (2011)
Taming the complexity of protein folding
Gregory R. Bowman et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)
Markov models of molecular kinetics: Generation and validation
Jan-Hendrik Prinz et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work
Hiroo Kenzaki et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Evolution of multisubunit RNA polymerases in the three domains of life
Finn Werner et al.
NATURE REVIEWS MICROBIOLOGY (2011)
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
Ignasi Buch et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein
Daniel-Adriano Silva et al.
PLOS COMPUTATIONAL BIOLOGY (2011)
One-step DNA melting in the RNA polymerase cleft opens the initiation bubble to form an unstable open complex
Theodore J. Gries et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Folding and binding cascades: Dynamic landscapes and population shifts
Sandeep Kumar et al.
PROTEIN SCIENCE (2010)
Improved side-chain torsion potentials for the Amber ff99SB protein force field
Kresten Lindorff-Larsen et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW
Faruck Morcos et al.
PLOS COMPUTATIONAL BIOLOGY (2010)
Principal component analysis
Herve Abdi et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL STATISTICS (2010)
Allosteric control of Escherichia coli rRNA promoter complexes by DksA
Steven T. Rutherford et al.
GENES & DEVELOPMENT (2009)
TRANSITION PATH THEORY FOR MARKOV JUMP PROCESSES
Philipp Metzner et al.
MULTISCALE MODELING & SIMULATION (2009)
Transcription inactivation through local refolding of the RNA polymerase structure
Georgiy A. Belogurov et al.
NATURE (2009)
Using generalized ensemble simulations and Markov state models to identify conformational states
Gregory R. Bowman et al.
METHODS (2009)
Rapid equilibrium sampling initiated from nonequilibrium data
Xuhui Huang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (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)
The RNA Polymerase Switch Region Is a Target for Inhibitors
Jayanta Mukhopadhyay et al.
CELL (2008)
Building Markov state models along pathways to determine free energies and rates of transitions
Albert C. Pan et al.
JOURNAL OF CHEMICAL PHYSICS (2008)
Coarse master equations for peptide folding dynamics
Nicolae-Viorel Buchete et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2008)
Intrinsic dynamics of enzymes in the unbound state and, relation to allosteric regulation
Ivet Bahar et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
Karunesh Arora 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)
Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism
Jennifer M. Bui et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations
Kei-ichi Okazaki et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Towards a theory of transition paths
Weinan E et al.
JOURNAL OF STATISTICAL PHYSICS (2006)
Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins
I Artsimovitch et al.
CELL (2005)
Robust Perron cluster analysis in conformation dynamics
P Deuflhard et al.
LINEAR ALGEBRA AND ITS APPLICATIONS (2005)
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
BY Ma et al.
PROTEIN SCIENCE (2002)
Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution
DG Vassylyev et al.
NATURE (2002)
Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution
KS Murakami et al.
SCIENCE (2002)
Structural basis of transcription:: RNA polymerase II at 2.8 Ångstrom resolution
P Cramer et al.
SCIENCE (2001)
Structural basis of transcription:: An RNA polymerase II elongation complex at 3.3 Å resolution
AL Gnatt et al.
SCIENCE (2001)
分享论文
