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

SRC: A Century of Science Brought to the Clinic

(2015) Alexey Aleshin et al.   NEOPLASIA

Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop

(2013) Yilin Meng et al.   JOURNAL OF MOLECULAR BIOLOGY

NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model-Free Framework and Markov State Simulations

(2013) Junchao Xia 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

Explaining why Gleevec is a specific and potent inhibitor of Abl kinase

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

Strategies for the Selective Regulation of Kinases with Allosteric Modulators: Exploiting Exclusive Structural Features

(2012) Zhizhou Fang et al.   ACS Chemical Biology

Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization

(2012) Yibing Shan et al.   CELL

A Novel Approach to the Discovery of Small-Molecule Ligands of CDK2

(2012) Mathew P. Martin et al.   CHEMBIOCHEM

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

New Insights in Protein Kinase Conformational Dynamics

(2012) Giorgio Saladino et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

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

Discovery of a Potential Allosteric Ligand Binding Site in CDK2

(2011) Stephane Betzi et al.   ACS Chemical Biology

The rise and fall of gatekeeper mutations? TheBCR-ABL1T315I paradigm

(2011) Don L. Gibbons et al.   CANCER

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

Characterization and Rapid Sampling of Protein Folding Markov State Model Topologies

(2011) Jeffrey K. Weber et al.   Journal of Chemical Theory and Computation

Insights into the Dynamics of HIV-1 Protease: A Kinetic Network Model Constructed from Atomistic Simulations

(2011) Nan-jie Deng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Proteus in the World of Proteins: Conformational Changes in Protein Kinases

(2010) Matthias Rabiller et al.   ARCHIV DER PHARMAZIE

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

Myristoylation and Membrane Binding Regulate c-Src Stability and Kinase Activity

(2010) P. Patwardhan et al.   MOLECULAR AND CELLULAR BIOLOGY

Targeting Bcr–Abl by combining allosteric with ATP-binding-site inhibitors

(2010) Jianming Zhang et al.   NATURE

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

The interplay of structural information and functional studies in kinase drug design: insights from BCR-Abl

(2009) Michael J Eck et al.   CURRENT OPINION IN CELL BIOLOGY

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

(2009) Christopher L. McClendon et al.   Journal of Chemical Theory and Computation

Exploring Complex Protein−Ligand Recognition Mechanisms with Coarse Metadynamics

(2009) Matteo Masetti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations

(2009) Fabio Pietrucci et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Transition Path Theory for Markov Jump Processes

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

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

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

(2009) Fabrizio Marinelli et al.   PLoS Computational Biology

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

Building Markov state models along pathways to determine free energies and rates of transitions

(2008) Albert C. Pan et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Identification ofN-(4-Piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H-pyrazole-3-carboxamide (AT7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design†

(2008) Paul G. Wyatt et al.   JOURNAL OF MEDICINAL CHEMISTRY

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

(2008) Anna Berteotti et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Tyr130 phosphorylation triggers Syk release from antigen receptor by long-distance conformational uncoupling

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

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