Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain

Identification of simple reaction coordinates from complex dynamics

(2017) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases

(2016) Nikita Chopra et al.   PLoS Computational Biology

Dynamics of Protein Kinases: Insights from Nuclear Magnetic Resonance

(2015) Yao Xiao et al.   ACCOUNTS OF CHEMICAL RESEARCH

The ABC of protein kinase conformations

(2015) Henrik Möbitz   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé et al.   Journal of Chemical Theory and Computation

Computational Study of the “DFG-Flip” Conformational Transition in c-Abl and c-Src Tyrosine Kinases

(2015) Yilin Meng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations

(2014) Mohammad M. Sultan et al.   Journal of Chemical Theory and Computation

Variational Approach to Molecular Kinetics

(2014) Feliks Nüske et al.   Journal of Chemical Theory and Computation

Phosphorylation releases constraints to domain motion in ERK2

(2014) Y. Xiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Diwakar Shukla et al.   Nature Communications

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

(2013) Marc W. van der Kamp et al.   BIOCHEMISTRY

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes 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

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

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

Transitions to catalytically inactive conformations in EGFR kinase

(2013) Y. Shan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Structural Basis for Control of Eukaryotic Protein Kinases

(2012) Jane A. Endicott et al.   Annual Review of Biochemistry

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

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

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation

(2012) Silvia Lovera et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

(2010) Vijay S. Pande et al.   METHODS

Insights into the conformational flexibility of Bruton's tyrosine kinase from multiple ligand complex structures

(2010) Andreas Kuglstatter et al.   PROTEIN SCIENCE

Protein kinases: evolution of dynamic regulatory proteins

(2010) Susan S. Taylor et al.   TRENDS IN BIOCHEMICAL SCIENCES

Atomistic View of the Conformational Activation of Src Kinase Using the String Method with Swarms-of-Trajectories

(2009) Wenxun Gan et al.   BIOPHYSICAL JOURNAL

Bruton’s tyrosine kinase (Btk): function, regulation, and transformation with special emphasis on the PH domain

(2009) Abdalla J. Mohamed et al.   IMMUNOLOGICAL REVIEWS

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

Transition networks for modeling the kinetics of conformational change in macromolecules

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

A conserved protonation-dependent switch controls drug binding in the Abl kinase

(2008) Y. Shan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An electrostatic network and long-range regulation of Src kinases

(2008) Elif Ozkirimli et al.   PROTEIN SCIENCE

Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms

(2008) Sichun Yang et al.   PLoS Computational Biology