Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs

Differential Effects of CSF-1R D802V and KIT D816V Homologous Mutations on Receptor Tertiary Structure and Allosteric Communication

(2014) Priscila Da Silva Figueiredo Celestino Gomes et al.   PLoS One

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

SPACER: server for predicting allosteric communication and effects of regulation

(2013) Alexander Goncearenco et al.   NUCLEIC ACIDS RESEARCH

PainNetworks: A web-based resource for the visualisation of pain-related genes in the context of their network associations

(2013) James R. Perkins et al.   PAIN

The spatial structure of cell signaling systems

(2013) Ruth Nussinov   PHYSICAL BIOLOGY

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

(2012) Cyrille Lepoivre et al.   BMC BIOINFORMATICS

xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures.

(2012) Marco Pasi et al.   Journal of Chemical Information and Modeling

Topological analysis and interactive visualization of biological networks and protein structures

(2012) Nadezhda T Doncheva et al.   Nature Protocols

Allosteric Communication across the Native and Mutated KIT Receptor Tyrosine Kinase

(2012) Elodie Laine et al.   PLoS Computational Biology

Allosteric Communication in Cysteinyl tRNA Synthetase

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

Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5

(2011) Mark J. Abraham et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Four-dimensional visualisation and analysis of protein-protein interaction networks

(2011) Apurv Goel et al.   PROTEOMICS

Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases

(2011) Anshuman Dixit et al.   PLoS Computational Biology

Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms

(2011) Elodie Laine et al.   PLoS Computational Biology

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Mechanisms of STAT Protein Activation by Oncogenic KIT Mutants in Neoplastic Mast Cells

(2010) Amandine Chaix et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms

(2009) Chung-Jung Tsai et al.   Molecular BioSystems

Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer

(2009) Giulia Morra et al.   PLoS Computational Biology

Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL

(2008) Chakra Chennubhotla et al.   Molecular BioSystems

Structural identification of the pathway of long-range communication in an allosteric enzyme

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

Allostery and cooperativity revisited

(2008) Qiang Cui et al.   PROTEIN SCIENCE