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

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

(2014) Vincent Frappier et al.   PLoS Computational Biology

DRoP: A Water Analysis Program Identifies Ras-GTP-Specific Pathway of Communication between Membrane-Interacting Regions and the Active Site

(2013) Bradley M. Kearney et al.   JOURNAL OF MOLECULAR BIOLOGY

Reconciling Mediating and Slaving Roles of Water in Protein Conformational Dynamics

(2013) Li Zhao et al.   PLoS One

Kinetic response of a photoperturbed allosteric protein

(2013) B. Buchli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles

(2012) Da-Wei Li et al.   JOURNAL OF BIOMOLECULAR NMR

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

Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

(2012) Elena Papaleo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2012) Elena Papaleo et al.   PLoS One

Dynamics in the Active Site of β-Secretase: A Network Analysis of Atomistic Simulations

(2011) Sabyashachi Mishra et al.   BIOCHEMISTRY

Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics

(2011) Alessandro Pandini et al.   FASEB JOURNAL

Allosteric Communication in Cysteinyl tRNA Synthetase

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

The flexible loop L1 of the H3K4 demethylase JARID1B ARID domain has a crucial role in DNA-binding activity

(2010) Wenming Yao et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Dimerization and ligand binding affect the structure network of A2A adenosine receptor

(2010) Francesca Fanelli et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Conserved amino acids participate in the structure networks deputed to intramolecular communication in the lutropin receptor

(2010) Krassimira Angelova et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

CCRXP: exploring clusters of conserved residues in protein structures

(2010) Shandar Ahmad et al.   NUCLEIC ACIDS RESEARCH

Intra and Inter-Molecular Communications Through Protein Structure Network

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

Structural waters define a functional channel mediating activation of the GPCR, rhodopsin

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

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Mechanisms of Inter- and Intramolecular Communication in GPCRs and G Proteins

(2008) Francesco Raimondi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Targeting the Human Cancer Pathway Protein Interaction Network by Structural Genomics

(2008) Yuanpeng Janet Huang et al.   MOLECULAR & CELLULAR PROTEOMICS