Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation

Activation Mechanism of Oncogenic Deletion Mutations in BRAF, EGFR, and HER2

(2016) Scott A. Foster et al.   CANCER CELL

Classification of small molecule protein kinase inhibitors based upon the structures of their drug-enzyme complexes

(2016) Robert Roskoski   PHARMACOLOGICAL RESEARCH

A Structural Perspective on the Regulation of the Epidermal Growth Factor Receptor

(2015) Erika Kovacs et al.   Annual Review of Biochemistry

Inhibition of RAF Isoforms and Active Dimers by LY3009120 Leads to Anti-tumor Activities in RAS or BRAF Mutant Cancers

(2015) Sheng-Bin Peng et al.   CANCER CELL

Structural Investigation of B-Raf Paradox Breaker and Inducer Inhibitors

(2015) Rohit Arora et al.   JOURNAL OF MEDICINAL CHEMISTRY

Small-world networks of residue interactions in the Abl kinase complexes with cancer drugs: topology of allosteric communication pathways can determine drug resistance effects

(2015) A. Tse et al.   Molecular BioSystems

RAF inhibitors that evade paradoxical MAPK pathway activation

(2015) Chao Zhang et al.   NATURE

Regulation of RAF protein kinases in ERK signalling

(2015) Hugo Lavoie et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A historical overview of protein kinases and their targeted small molecule inhibitors

(2015) Robert Roskoski   PHARMACOLOGICAL RESEARCH

Allosteric small-molecule kinase inhibitors

(2015) Peng Wu et al.   PHARMACOLOGY & THERAPEUTICS

Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

(2015) Amanda Tse et al.   PLoS One

Dynamics-Driven Allostery in Protein Kinases

(2015) Alexandr P. Kornev et al.   TRENDS IN BIOCHEMICAL SCIENCES

FDA-approved small-molecule kinase inhibitors

(2015) Peng Wu et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Molecular mechanisms of asymmetric RAF dimer activation

(2014) Pablo G. Jambrina et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Mechanism and consequences of RAF kinase activation by small-molecule inhibitors

(2014) M Holderfield et al.   BRITISH JOURNAL OF CANCER

Structure of the BRAF-MEK Complex Reveals a Kinase Activity Independent Role for BRAF in MAPK Signaling

(2014) Jacob R. Haling et al.   CANCER CELL

Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases

(2014) Sandra W Cowan-Jacob et al.   Future Medicinal Chemistry

Kinases and Pseudokinases: Lessons from RAF

(2014) A. S. Shaw et al.   MOLECULAR AND CELLULAR BIOLOGY

Crystal structure of a BRAF kinase domain monomer explains basis for allosteric regulation

(2014) Neroshan Thevakumaran et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ErbB/HER protein-tyrosine kinases: Structures and small molecule inhibitors

(2014) Robert Roskoski   PHARMACOLOGICAL RESEARCH

Dimerization-induced allostery in protein kinase regulation

(2014) Hugo Lavoie et al.   TRENDS IN BIOCHEMICAL SCIENCES

Emerging concepts in the regulation of the EGF receptor and other receptor tyrosine kinases

(2014) Nicholas F. Endres et al.   TRENDS IN BIOCHEMICAL SCIENCES

PKA: Lessons learned after twenty years

(2013) Susan S. Taylor et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Allosteric Activation of Functionally Asymmetric RAF Kinase Dimers

(2013) Jiancheng Hu et al.   CELL

Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories

(2013) Panagiotis I. Koukos et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Discovery and Optimization of a Novel Series of Potent Mutant B-RafV600E Selective Kinase Inhibitors

(2013) Melissa M. Vasbinder et al.   JOURNAL OF MEDICINAL CHEMISTRY

Inhibitors that stabilize a closed RAF kinase domain conformation induce dimerization

(2013) Hugo Lavoie et al.   Nature Chemical Biology

Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins

(2013) Kuan Pern Tan et al.   NUCLEIC ACIDS RESEARCH

The ErbB/HER family of protein-tyrosine kinases and cancer

(2013) Robert Roskoski   PHARMACOLOGICAL RESEARCH

Deciphering the Structural Basis of Eukaryotic Protein Kinase Regulation

(2013) Hiruy S. Meharena et al.   PLOS BIOLOGY

The Structural Basis for Control of Eukaryotic Protein Kinases

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

Assessing the range of kinase autoinhibition mechanisms in the insulin receptor family

(2012) Stephen C. Artim et al.   BIOCHEMICAL JOURNAL

Measuring and comparing structural fluctuation patterns in large protein datasets

(2012) Edvin Fuglebakk et al.   BIOINFORMATICS

αC helix displacement as a general approach for allosteric modulation of protein kinases

(2012) Lorenzo Palmieri et al.   DRUG DISCOVERY TODAY

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Identification of a Novel Family of BRAFV600E Inhibitors

(2012) Jie Qin et al.   JOURNAL OF MEDICINAL CHEMISTRY

Assembly of allosteric macromolecular switches: lessons from PKA

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

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

Design principles underpinning the regulatory diversity of protein kinases

(2012) K. Oruganty et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolution of the eukaryotic protein kinases as dynamic molecular switches

(2012) S. S. Taylor et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Evolution of Protein Kinase Inhibitors from Antagonists to Agonists of Cellular Signaling

(2011) Arvin C. Dar et al.   Annual Review of Biochemistry

Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism

(2011) Moitrayee Bhattacharyya et al.   BIOCHEMISTRY

Regulation of the catalytic activity of the EGF receptor

(2011) Nicholas F Endres et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Allosteric Communication in Cysteinyl tRNA Synthetase

(2011) Amit Ghosh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Catalytic Control in the EGF Receptor and Its Connection to General Kinase Regulatory Mechanisms

(2011) Natalia Jura et al.   MOLECULAR CELL

RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E)

(2011) Poulikos I. Poulikakos et al.   NATURE

The Dichotomy in Degree Correlation of Biological Networks

(2011) Dapeng Hao et al.   PLoS One

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

RAF protein-serine/threonine kinases: Structure and regulation

(2010) Robert Roskoski   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Non-oxime inhibitors of B-RafV600E kinase

(2010) Li Ren et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Non-oxime pyrazole based inhibitors of B-Raf kinase

(2010) Bradley J. Newhouse et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Interaction Energy Based Protein Structure Networks

(2010) M.S. Vijayabaskar et al.   BIOPHYSICAL JOURNAL

Kinase-Dead BRAF and Oncogenic RAS Cooperate to Drive Tumor Progression through CRAF

(2010) Sonja J. Heidorn et al.   CELL

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Mechanistic principles of RAF kinase signaling

(2010) Christian M. Udell et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Protein kinase signaling networks in cancer

(2010) John Brognard et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Asymmetric tyrosine kinase arrangements in activation or autophosphorylation of receptor tyrosine kinases

(2010) Jae Hyun Bae et al.   MOLECULES AND CELLS

RAF inhibitors transactivate RAF dimers and ERK signalling in cells with wild-type BRAF

(2010) Poulikos I. Poulikakos et al.   NATURE

RAF inhibitors prime wild-type RAF to activate the MAPK pathway and enhance growth

(2010) Georgia Hatzivassiliou et al.   NATURE

Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma

(2010) Gideon Bollag et al.   NATURE

WIWS: a protein structure bioinformatics Web service collection

(2010) M. L. Hekkelman et al.   NUCLEIC ACIDS RESEARCH

Protein kinases: evolution of dynamic regulatory proteins

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

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

(2010) Moitrayee Bhattacharyya et al.   BMC STRUCTURAL BIOLOGY

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

(2010) Sumeet Agarwal et al.   PLoS Computational Biology

The Crystal Structure of BRAF in Complex with an Organoruthenium Inhibitor Reveals a Mechanism for Inhibition of an Active Form of BRAF Kinase

(2009) Peng Xie et al.   BIOCHEMISTRY

Tyrosine phosphorylation: thirty years and counting

(2009) Tony Hunter   CURRENT OPINION IN CELL BIOLOGY

A dimerization-dependent mechanism drives RAF catalytic activation

(2009) Thanashan Rajakulendran et al.   NATURE

Dynamical networks in tRNA:protein complexes

(2009) A. Sethi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure-Based View of Epidermal Growth Factor Receptor Regulation

(2008) Kathryn M. Ferguson   Annual Review of Biophysics

Variations in Clique and Community Patterns in Protein Structures during Allosteric Communication: Investigation of Dynamically Equilibrated Structures of Methionyl tRNA Synthetase Complexes†

(2008) Amit Ghosh et al.   BIOCHEMISTRY

Potent and selective pyrazole-based inhibitors of B-Raf kinase

(2008) Joshua D. Hansen et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

The ErbB kinase domain: Structural perspectives into kinase activation and inhibition

(2008) Ron Bose et al.   EXPERIMENTAL CELL RESEARCH

Ligand-induced ErbB receptor dimerization

(2008) Mark A. Lemmon   EXPERIMENTAL CELL RESEARCH

A helix scaffold for the assembly of active protein kinases

(2008) A. P. Kornev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity

(2008) J. Tsai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved spatial patterns across the protein kinase family

(2007) Lynn F. Ten Eyck et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS