NAPS: Network Analysis of Protein Structures

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

Modeling proteins as residue interaction networks

(2015) Rajdeep Grewal et al.   PROTEIN AND PEPTIDE LETTERS

CyToStruct: Augmenting the Network Visualization of Cytoscape with the Power of Molecular Viewers

(2015) Sergey Nepomnyachiy et al.   STRUCTURE

The construction of an amino acid network for understanding protein structure and function

(2014) Wenying Yan et al.   AMINO ACIDS

ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures

(2014) Thomas Hrabe et al.   BMC BIOINFORMATICS

A graph theoretic approach to utilizing protein structure to identify non-random somatic mutations

(2014) Gregory A Ryslik et al.   BMC BIOINFORMATICS

Identifying tandem Ankyrin repeats in protein structures

(2014) Broto Chakrabarty et al.   BMC BIOINFORMATICS

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

Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications

(2014) Kristin Blacklock et al.   PLoS Computational Biology

PRIGSA: Protein repeat identification by graph spectral analysis

(2014) Broto Chakrabarty et al.   Journal of Bioinformatics and Computational Biology

JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied toProteopedia

(2013) Robert M. Hanson et al.   ISRAEL JOURNAL OF CHEMISTRY

Protein structure networks

(2012) L. H. Greene   Briefings in Functional Genomics

Protein Contact Networks: An Emerging Paradigm in Chemistry

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

Proteins as Sponges: A Statistical Journey along Protein Structure Organization Principles

(2012) Luisa Di Paola et al.   Journal of Chemical Information and Modeling

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

CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods

(2012) D. Kozma et al.   NUCLEIC ACIDS RESEARCH

RING: networking interacting residues, evolutionary information and energetics in protein structures

(2011) A. J. M. Martin et al.   BIOINFORMATICS

CMView: Interactive contact map visualization and analysis

(2011) C. Vehlow et al.   BIOINFORMATICS

Analyzing and visualizing residue networks of protein structures

(2011) Nadezhda T. Doncheva et al.   TRENDS IN BIOCHEMICAL SCIENCES

Universality in Protein Residue Networks

(2010) Ernesto Estrada   BIOPHYSICAL JOURNAL

Optimal contact definition for reconstruction of Contact Maps

(2010) Jose M Duarte et al.   BMC BIOINFORMATICS

AMINONET– a tool to construct and visualize amino acid networks, and to calculate topological parameters

(2010) Md. Aftabuddin et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Understanding Protein Structure from a Percolation Perspective

(2009) Dhruba Deb et al.   BIOPHYSICAL JOURNAL

Intra and Inter-Molecular Communications Through Protein Structure Network

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

Analysis of protein folds using protein contact networks

(2009) Pankaj Barah et al.   PRAMANA-JOURNAL OF PHYSICS

Variations in Clique and Community Patterns in Protein Structures during Allosteric Communication: Investigation of Dynamically Equilibrated Structures of Methionyl tRNA Synthetase Complexes†

(2008) Amit Ghosh et al.   BIOCHEMISTRY

Insights into Protein–DNA Interactions through Structure Network Analysis

(2008) R. Sathyapriya et al.   PLoS Computational Biology