A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation

Systematically Constructing Kinetic Transition Network in Polypeptide from Top to Down: Trajectory Mapping

(2015) Linchen Gong et al.   PLoS One

A Critical Residue Selectively Recruits Nucleotides for T7 RNA Polymerase Transcription Fidelity Control

(2014) Baogen Duan et al.   BIOPHYSICAL JOURNAL

Bacteriophage-based synthetic biology for the study of infectious diseases

(2014) Robert J Citorik et al.   CURRENT OPINION IN MICROBIOLOGY

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1

(2014) Om P Choudhary et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

(2014) D.-A. Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I

(2014) Bill R. Miller et al.   PLoS Computational Biology

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

Analysis Tool Web Services from the EMBL-EBI

(2013) Hamish McWilliam et al.   NUCLEIC ACIDS RESEARCH

The RNA polymerase trigger loop functions in all three phases of the transcription cycle

(2013) T. Fouqueau et al.   NUCLEIC ACIDS RESEARCH

A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase

(2013) Lin-Tai Da et al.   PLoS Computational Biology

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

(2013) Manchuta Dangkulwanich et al.   eLife

A Small Post-Translocation Energy Bias Aids Nucleotide Selection in T7 RNA Polymerase Transcription

(2012) Jin Yu et al.   BIOPHYSICAL JOURNAL

Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms

(2012) Tamar Schlick et al.   THEORETICAL CHEMISTRY ACCOUNTS

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

(2011) Wei Zhuang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories

(2011) Thomas J. Lane et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II

(2011) Lin-Tai Da et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein

(2011) Daniel-Adriano Silva et al.   PLoS Computational Biology

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

(2010) François-Yves Dupradeau et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis

(2010) Andrei A. Golosov et al.   STRUCTURE

The structural changes of T7 RNA polymerase from transcription initiation to elongation

(2009) Thomas A Steitz   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

(2009) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase

(2009) Guo-Qing Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid equilibrium sampling initiated from nonequilibrium data

(2009) X. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

T7 RNA Polymerase Studied by Force Measurements Varying Cofactor Concentration

(2008) P. Thomen et al.   BIOPHYSICAL JOURNAL

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Molecular dynamics studies of the energetics of translocation in model T7 RNA polymerase elongation complexes

(2008) Hyung-June Woo et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

RNA polymerase: the vehicle of transcription

(2008) Sergei Borukhov et al.   TRENDS IN MICROBIOLOGY