Dissecting protein architecture with communication blocks and communicating segment pairs

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

A dynamically coupled allosteric network underlies binding cooperativity in Src kinase

(2015) Zachariah H. Foda et al.   Nature Communications

Integrating protein structural dynamics and evolutionary analysis with Bio3D

(2014) Lars Skjærven et al.   BMC BIOINFORMATICS

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2014) Ariane Allain et al.   FARADAY DISCUSSIONS

PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins

(2014) Matteo Tiberti et al.   Journal of Chemical Information and Modeling

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

Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity

(2014) Isaure Chauvot de Beauchêne et al.   PLoS Computational Biology

Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops

(2014) Gaetano Invernizzi et al.   PLoS Computational Biology

GSATools: analysis of allosteric communication and functional local motions using a structural alphabet

(2013) Alessandro Pandini et al.   BIOINFORMATICS

A Mixed Protein Structure Network and Elastic Network Model Approach to Predict the Structural Communication in Biomolecular Systems: The PDZ2 Domain from Tyrosine Phosphatase 1E As a Case Study

(2013) Francesco Raimondi et al.   Journal of Chemical Theory and Computation

PDBsum additions

(2013) Tjaart A. P. de Beer et al.   NUCLEIC ACIDS RESEARCH

Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study

(2013) Kristin Blacklock et al.   PLoS One

Mapping the Structural and Dynamical Features of Multiple p53 DNA Binding Domains: Insights into Loop 1 Intrinsic Dynamics

(2013) Suryani Lukman et al.   PLoS One

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

Tumor Suppression in the Absence of p53-Mediated Cell-Cycle Arrest, Apoptosis, and Senescence

(2012) Tongyuan Li et al.   CELL

Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

(2012) Elena Papaleo et al.   PLoS One

Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations

(2012) Federica Chiappori et al.   PLoS Computational Biology

Allosteric Communication across the Native and Mutated KIT Receptor Tyrosine Kinase

(2012) Elodie Laine et al.   PLoS Computational Biology

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

Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces

(2010) Michele Seeber et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Blinded by the Light: The Growing Complexity of p53

(2009) Karen H. Vousden et al.   CELL

Structural biology of the p53 tumour suppressor

(2009) Andrei L Okorokov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Intra and Inter-Molecular Communications Through Protein Structure Network

(2009) Saraswathi Vishveshwara et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations

(2009) Willy Wriggers et al.   Journal of Chemical Theory and Computation

Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins

(2009) T. P. Schrank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients

(2009) K. S. Gajiwala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

(2008) Hongxing Lei et al.   JOURNAL OF CHEMICAL PHYSICS

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY