Allostery through the computational microscope: cAMP activation of a canonical signalling domain

Cyclic Nucleotide Mapping of Hyperpolarization-Activated Cyclic Nucleotide-Gated (HCN) Channels

(2014) Stefan Möller et al.   ACS Chemical Biology

Markov state models of biomolecular conformational dynamics

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

Computational approaches to mapping allosteric pathways

(2014) Victoria A Feher et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Using Markov State Models to Develop a Mechanistic Understanding of Protein Kinase A Regulatory Subunit RIα Activation in Response to cAMP Binding

(2014) Britton W. Boras et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Application of Molecular-Dynamics Based Markov State Models to Functional Proteins

(2014) Robert D. Malmstrom et al.   Journal of Chemical Theory and Computation

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

Emerging computational approaches for the study of protein allostery

(2013) Galen Collier et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Ultrasonic and Densimetric Characterization of the Association of Cyclic AMP with the cAMP-Binding Domain of the Exchange Protein EPAC1

(2013) Ikbae Son et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Signaling through dynamic linkers as revealed by PKA

(2013) M. Akimoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accounting for the kinetics in order parameter analysis: Lessons from theoretical models and a disordered peptide

(2012) Ganna Berezovska et al.   JOURNAL OF CHEMICAL PHYSICS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Assembly of allosteric macromolecular switches: lessons from PKA

(2012) Susan S. Taylor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structure-based model of allostery predicts coupling between distant sites

(2012) P. Weinkam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

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

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

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables

(2011) Jan-Hendrik Prinz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

From Induced Fit to Conformational Selection: A Continuum of Binding Mechanism Controlled by the Timescale of Conformational Transitions

(2010) Huan-Xiang Zhou   BIOPHYSICAL JOURNAL

Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models

(2010) Gregory R. Bowman et al.   Journal of Chemical Theory and Computation

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

(2010) Vijay S. Pande et al.   METHODS

Cyclic AMP- and (Rp)-cAMPS-induced Conformational Changes in a Complex of the Catalytic and Regulatory (RIα) Subunits of Cyclic AMP-dependent Protein Kinase

(2010) Ganesh S. Anand et al.   MOLECULAR & CELLULAR PROTEOMICS

Cyclic AMP Analog Blocks Kinase Activation by Stabilizing Inactive Conformation: Conformational Selection Highlights a New Concept in Allosteric Inhibitor Design

(2010) Suguna Badireddy et al.   MOLECULAR & CELLULAR PROTEOMICS

Dissecting the cAMP-inducible allosteric switch in protein kinase A RIα

(2010) Timothy J. Sjoberg et al.   PROTEIN SCIENCE

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

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

(2009) Gregory R. Bowman et al.   METHODS

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories

(2009) S. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

(2008) Alexandros Altis et al.   JOURNAL OF CHEMICAL PHYSICS

Allostery and cooperativity revisited

(2008) Qiang Cui et al.   PROTEIN SCIENCE

A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains

(2008) Alexandr P. Kornev et al.   PLoS Computational Biology