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

Decoding the Host–Parasite Protein Interactions Involved in Cerebral Malaria Through Glares of Molecular Dynamics Simulations

(2022) Omkar Indari et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unraveling the Molecular Mechanism of Recognition of Selected Next-Generation Antirheumatoid Arthritis Inhibitors by Janus Kinase 1

(2022) Md Fulbabu Sk et al.   ACS Omega

Phosphorylation, Mg-ADP, and Inhibitors Differentially Shape the Conformational Dynamics of the A-Loop of Aurora-A

(2021) Zahra Musavizadeh et al.   Biomolecules

Identification of Potential Inhibitors against Epstein–Barr Virus Nuclear Antigen 1 (EBNA1): An Insight from Docking and Molecular Dynamic Simulations

(2021) Shweta Jakhmola et al.   ACS Chemical Neuroscience

Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study

(2021) Rajarshi Roy et al.   Journal of Chemical Information and Modeling

Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study

(2021) M.F. Sk et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV

(2020) Timothy P. Sheahan et al.   Nature Communications

Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations

(2020) Md Fulbabu Sk et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

(2020) Angelo Felline et al.   NUCLEIC ACIDS RESEARCH

Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations

(2020) Md Fulbabu Sk et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Conformational states dynamically populated by a kinase determine its function

(2020) Tao Xie et al.   SCIENCE

Structural Basis for Targeting the Folded P-Loop Conformation of c-MET

(2020) Gavin W. Collie et al.   ACS Medicinal Chemistry Letters

Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM

(2020) Md Fulbabu Sk et al.   Frontiers in Molecular Biosciences

How Electrostatic Coupling Enables Conformational Plasticity in a Tyrosine Kinase

(2019) Cheng-Chieh Tsai et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

The molecular basis of JAK/STAT inhibition by SOCS1

(2018) Nicholas P. D. Liau et al.   Nature Communications

New insights into the structural dynamics of the kinase JNK3

(2018) Pankaj Mishra et al.   Scientific Reports

Avoiding False Positive Conclusions in Molecular Simulation: The Importance of Replicas

(2018) Bernhard Knapp 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

Insight into binding mechanisms of inhibitors MKP56, MKP73, MKP86, and MKP97 to HIV-1 protease by using molecular dynamics simulation

(2017) Shuhua Shi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

The Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of a TYK2/JAK1 Inhibitor (PF-06700841) in Healthy Subjects and Patients With Plaque Psoriasis

(2017) Christopher Banfield et al.   JOURNAL OF CLINICAL PHARMACOLOGY

Downregulated SOCS1 expression activates the JAK1/STAT1 pathway and promotes polarization of macrophages into M1 type

(2017) Yan-Bing Liang et al.   Molecular Medicine Reports

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

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

Computational Studies of a Mechanism for Binding and Drug Resistance in the Wild Type and Four Mutations of HIV-1 Protease with a GRL-0519 Inhibitor

(2016) Guodong Hu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

Discovery of VX-509 (Decernotinib): A Potent and Selective Janus Kinase 3 Inhibitor for the Treatment of Autoimmune Diseases

(2015) Luc J. Farmer et al.   JOURNAL OF MEDICINAL CHEMISTRY

Modeling Proteins as Residue Interaction Networks to Understand Structure-Function Relationship

(2015) Isha D. Mehta et al.   BIOPHYSICAL JOURNAL

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

(2014) Diwakar Shukla et al.   Nature Communications

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

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

Suppression of cytokine signaling: The SOCS perspective

(2013) Edmond M. Linossi et al.   CYTOKINE & GROWTH FACTOR REVIEWS

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

Buried and Accessible Surface Area Control Intrinsic Protein Flexibility

(2013) Joseph A. Marsh   JOURNAL OF MOLECULAR BIOLOGY

SOCS3 binds specific receptor–JAK complexes to control cytokine signaling by direct kinase inhibition

(2013) Nadia J Kershaw et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Deciphering the Structural Basis of Eukaryotic Protein Kinase Regulation

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

Protein Contact Networks: An Emerging Paradigm in Chemistry

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

JAK's SOCS: A Mechanism of Inhibition

(2012) Akihiko Yoshimura et al.   IMMUNITY

Suppression of Cytokine Signaling by SOCS3: Characterization of the Mode of Inhibition and the Basis of Its Specificity

(2012) Jeffrey J. Babon et al.   IMMUNITY

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

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

Protein kinases: evolution of dynamic regulatory proteins

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

Equally Potent Inhibition of c-Src and Abl by Compounds that Recognize Inactive Kinase Conformations

(2009) M. A. Seeliger et al.   CANCER RESEARCH

Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA

(2009) Giulio Rastelli et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Identification of novel epigenetically modified genes in human melanoma via promoter methylation gene profiling

(2008) Suhu Liu et al.   Pigment Cell & Melanoma Research