Activating mutations drive human MEK1 kinase using a gear-shifting mechanism

Qualitative differences in disease-associated MEK mutants reveal molecular signatures and aberrant signaling-crosstalk in cancer

(2022) Yuji Kubota et al.   Nature Communications

Computational studies of anaplastic lymphoma kinase mutations reveal common mechanisms of oncogenic activation

(2021) Keshav Patil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine learning approaches for analyzing and enhancing molecular dynamics simulations

(2020) Yihang Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural basis for the action of the drug trametinib at KSR-bound MEK

(2020) Zaigham M. Khan et al.   NATURE

Conformational states dynamically populated by a kinase determine its function

(2020) Tao Xie et al.   SCIENCE

Unified Approach to Enhanced Sampling

(2020) Michele Invernizzi et al.   Physical Review X

Conformational Dynamics Analysis of MEK1 Using Hydrogen/Deuterium Exchange Mass Spectrometry

(2020) Min Woo Yun et al.   PROTEIN AND PEPTIDE LETTERS

Targeting Alterations in the RAF–MEK Pathway

(2019) Rona Yaeger et al.   Cancer Discovery

Multithermal-Multibaric Molecular Simulations from a Variational Principle

(2019) Pablo M. Piaggi et al.   PHYSICAL REVIEW LETTERS

Computational algorithms for in silico profiling of activating mutations in cancer

(2019) E. Joseph Jordan et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Optimizing photoswitchable MEK

(2019) Aleena L. Patel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transferable Neural Networks for Enhanced Sampling of Protein Dynamics

(2018) Mohammad M. Sultan et al.   Journal of Chemical Theory and Computation

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

(2018) Carlos HM Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Tailoring the oxygenated groups of graphene hydrogels for high-performance supercapacitors with large areal mass loadings

(2018) Hongyun Ma et al.   Journal of Materials Chemistry A

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling

(2018) Tatu Pantsar et al.   PLoS Computational Biology

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Quantitative conformational profiling of kinase inhibitors reveals origins of selectivity for Aurora kinase activation states

(2018) Eric W. Lake et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review)

(2017) Fatima Ardito et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

PAK signalling drives acquired drug resistance to MAPK inhibitors in BRAF-mutant melanomas

(2017) Hezhe Lu et al.   NATURE

In vivo severity ranking of Ras pathway mutations associated with developmental disorders

(2017) Granton A. Jindal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Frequency modulation of ERK activation dynamics rewires cell fate

(2015) H. Ryu et al.   Molecular Systems Biology

Cell signaling and transcription factors regulating cell fate during formation of the mouse blastocyst

(2015) Tristan Frum et al.   TRENDS IN GENETICS

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

Targeting Conformational Plasticity of Protein Kinases

(2014) Michael Tong et al.   ACS Chemical Biology

Computational delineation of tyrosyl-substrate recognition and catalytic landscapes by the epidermal growth factor receptor tyrosine kinase domain

(2014) Yingting Liu et al.   Molecular BioSystems

The clinical development of MEK inhibitors

(2014) Yujie Zhao et al.   Nature Reviews Clinical Oncology

Targeting RAS–ERK signalling in cancer: promises and challenges

(2014) Ahmed A. Samatar et al.   NATURE REVIEWS DRUG DISCOVERY

The RASopathies

(2013) Katherine A. Rauen   Annual Review of Genomics and Human Genetics

Characterization of Rare Events in Molecular Dynamics

(2013) Carsten Hartmann et al.   Entropy

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition

(2013) N. Wagle et al.   Cancer Discovery

Deciphering the Structural Basis of Eukaryotic Protein Kinase Regulation

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

Erlotinib binds both inactive and active conformations of the EGFR tyrosine kinase domain

(2012) Jin H. Park et al.   BIOCHEMICAL JOURNAL

Signaling Mechanisms Controlling Cell Fate and Embryonic Patterning

(2012) N. Perrimon et al.   Cold Spring Harbor Perspectives in Biology

Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases

(2011) Andrew J. Shih et al.   BIOCHEMICAL JOURNAL

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Structures of human MST3 kinase in complex with adenine, ADP and Mn2+

(2010) Tzu-Ping Ko et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

(2010) Pär Bjelkmar et al.   Journal of Chemical Theory and Computation

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

(2010) C. F. Abrams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal Structures of MEK1 Binary and Ternary Complexes with Nucleotides and Inhibitors

(2009) Thierry O. Fischmann et al.   BIOCHEMISTRY

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

MEK1 mutations confer resistance to MEK and B-RAF inhibition

(2009) C. M. Emery et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Sending Signals Dynamically

(2009) R. G. Smock et al.   SCIENCE

Molecular simulations of protein dynamics: new windows on mechanisms in biology

(2008) Guy G Dodson et al.   EMBO REPORTS

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS