Molecular dynamics simulations reveal phosphorylation-induced conformational dynamics of the fibroblast growth factor receptor 1 kinase

Phosphorylation-Induced Conformational Dynamics and Inhibition of Janus Kinase 1 by Suppressors of Cytokine Signaling 1

(2022) Md Fulbabu Sk et al.   JOURNAL OF PHYSICAL CHEMISTRY B

webPSN v2.0: a webserver to infer fingerprints of structural communication in biomacromolecules

(2020) Angelo Felline et al.   NUCLEIC ACIDS RESEARCH

Conformational states dynamically populated by a kinase determine its function

(2020) Tao Xie et al.   SCIENCE

Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations

(2019) Nisha A. Jonniya et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Investigating Phosphorylation-Induced Conformational Changes in WNK1 Kinase by Molecular Dynamics Simulations

(2019) Nisha Amarnath Jonniya et al.   ACS Omega

Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models

(2018) Yilin Meng et al.   Journal of Chemical Theory and Computation

Long-range molecular dynamics show that inactive forms of Protein Kinase A are more dynamic than active forms

(2018) R. Kalaivani et al.   PROTEIN SCIENCE

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Dynamic, structural and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation

(2017) Yaozong Li et al.   Chemical Science

Effects of FGFR2 kinase activation loop dynamics on catalytic activity

(2017) Jerome M. Karp et al.   PLoS Computational Biology

Molecular Dynamics Simulations and Structural Network Analysis of c-Abl and c-Src Kinase Core Proteins: Capturing Allosteric Mechanisms and Communication Pathways from Residue Centrality

(2015) Amanda Tse et al.   Journal of Chemical Information and Modeling

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Structural and dynamic insights into the energetics of activation loop rearrangement in FGFR1 kinase

(2015) Tobias Klein et al.   Nature Communications

The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study

(2015) Tom D. Bunney et al.   EBioMedicine

Dynamic architecture of a protein kinase

(2014) C. L. McClendon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Structural dynamic analysis of apo and ATP-bound IRAK4 kinase

(2014) Vijayakumar Gosu et al.   Scientific Reports

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

(2014) Huiyong Sun et al.   PLoS Computational Biology

Kinase Drug Discovery – What’s Next in the Field?

(2013) Philip Cohen et al.   ACS Chemical Biology

Normal mode analysis based on an elastic network model for biomolecules in the Protein Data Bank, which uses dihedral angles as independent variables

(2013) Hiroshi Wako et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

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

Cracking the Molecular Origin of Intrinsic Tyrosine Kinase Activity through Analysis of Pathogenic Gain-of-Function Mutations

(2013) Huaibin Chen et al.   Cell Reports

Tyrosine Kinase Inhibitors: Views of Selectivity, Sensitivity, and Clinical Performance

(2012) Alexander Levitzki   Annual Review of Pharmacology and Toxicology

Mechanisms of FGFR-mediated carcinogenesis

(2012) Imran Ahmad et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Protein Contact Networks: An Emerging Paradigm in Chemistry

(2012) L. Di Paola et al.   CHEMICAL REVIEWS

Fibroblast growth factor receptors in breast cancer: expression, downstream effects, and possible drug targets

(2012) M Tenhagen et al.   ENDOCRINE-RELATED CANCER

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

An overview of the Amber biomolecular simulation package

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

Understanding the Impact of the P-loop Conformation on Kinase Selectivity

(2011) Cristiano R. W. Guimarães et al.   Journal of Chemical Information and Modeling

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

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

(2011) Natalia Jura et al.   MOLECULAR CELL

Inhibitor-Sensitive FGFR1 Amplification in Human Non-Small Cell Lung Cancer

(2011) Amit Dutt et al.   PLoS One

Targeting mutant fibroblast growth factor receptors in cancer

(2011) Heidi Greulich et al.   TRENDS IN MOLECULAR MEDICINE

FGFR1 Amplification Drives Endocrine Therapy Resistance and Is a Therapeutic Target in Breast Cancer

(2010) N. Turner et al.   CANCER RESEARCH

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Protein kinases: evolution of dynamic regulatory proteins

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

The Precise Sequence of FGF Receptor Autophosphorylation Is Kinetically Driven and Is Disrupted by Oncogenic Mutations

(2009) E. D. Lew et al.   Science Signaling

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

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

A crystallographic snapshot of tyrosine trans-phosphorylation in action

(2008) H. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA