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

statnet: Software Tools for the Representation, Visualization, Analysis and Simulation of Network Data

(2015) Mark S. Handcock et al.   Journal of Statistical Software

Amino Acid Network for the Discrimination of Native Protein Structures from Decoys

(2014) Jianhong Zhou et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Evolution of protein structures and interactions from the perspective of residue contact networks

(2013) Xiuwei Zhang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Potential Application of Network Descriptions for Understanding Conformational Changes and Protonation States of ABC Transporters

(2013) Tamas Hegedus et al.   CURRENT PHARMACEUTICAL DESIGN

The Topology and Dynamics of Protein Complexes: Insights from Intra– Molecular Network Theory

(2013) Guang Hu et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis

(2013) Jiajia Chen et al.   Journal of Translational Medicine

Perturbation Centrality and Turbine: A Novel Centrality Measure Obtained Using a Versatile Network Dynamics Tool

(2013) Kristóf Z. Szalay et al.   PLoS One

NetworkView: 3D display and analysis of protein{middle dot}RNA interaction networks

(2012) J. Eargle et al.   BIOINFORMATICS

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

Yeast Network and Report of New Stochastic-Credibility Cell Cycle Models

(2012) Oana Chis et al.   Current Bioinformatics

Disordered Proteins and Network Disorder in Network Descriptions of Protein Structure, Dynamics and Function: Hypotheses and a Comprehensive Review

(2012) Peter Csermely et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Network properties of protein-decoy structures

(2012) Subhojyoti Chatterjee et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

Exploring Residue Component Contributions to Dynamical Network Models of Allostery

(2012) Adam T. VanWart et al.   Journal of Chemical Theory and Computation

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

Topological analysis and interactive visualization of biological networks and protein structures

(2012) Nadezhda T Doncheva et al.   Nature Protocols

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

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

Modeling allosteric signal propagation using protein structure networks

(2011) Keunwan Park et al.   BMC BIOINFORMATICS

Predicting disease-associated substitution of a single amino acid by analyzing residue interactions

(2011) Yizhou Li et al.   BMC BIOINFORMATICS

Scoring Function Based on Weighted Residue Network

(2011) Xiong Jiao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

JGromacs: A Java Package for Analyzing Protein Simulations

(2011) Márton Münz et al.   Journal of Chemical Information and Modeling

Novel Feature for Catalytic Protein Residues Reflecting Interactions with Other Residues

(2011) Yizhou Li et al.   PLoS One

Towards an integrated understanding of the structural characteristics of protein residue networks

(2011) Susan Khor   THEORY IN BIOSCIENCES

Analyzing and visualizing residue networks of protein structures

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

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Universality in Protein Residue Networks

(2010) Ernesto Estrada   BIOPHYSICAL JOURNAL

Interaction Energy Based Protein Structure Networks

(2010) M.S. Vijayabaskar et al.   BIOPHYSICAL JOURNAL

Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern

(2010) Binhua Tang et al.   BMC Systems Biology

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

Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants

(2010) Francesca Fanelli et al.   FASEB JOURNAL

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

Computational Tools for the Interactive Exploration of Proteomic and Structural Data

(2010) John H. Morris et al.   MOLECULAR & CELLULAR PROTEOMICS

Effects of Time Point Measurement on the Reconstruction of Gene Regulatory Networks

(2010) Wenying Yan et al.   MOLECULES

Analysis and network representation of hotspots in protein interfaces using minimum cut trees

(2010) Nurcan Tuncbag et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks

(2009) Priti Hansia et al.   Molecular BioSystems

Residue network in protein native structure belongs to the universality class of a three-dimensional critical percolation cluster

(2009) Hidetoshi Morita et al.   PHYSICAL REVIEW E

Dynamical networks in tRNA:protein complexes

(2009) A. Sethi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Substrate uptake and protein stability relationship in mammalian histidine decarboxylase

(2009) A. Pino-Ángeles et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A graph theoretic approach to protein structure selection

(2008) Marco Vassura et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

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

Amino acid network and its scoring application in protein–protein docking

(2008) Shan Chang et al.   BIOPHYSICAL CHEMISTRY

Cutoff variation induces different topological properties: A new discovery of amino acid network within protein

(2008) Tao Yu et al.   JOURNAL OF THEORETICAL BIOLOGY

Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction

(2008) Vagmita Pabuwal et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins

(2008) Carlos H. da Silveira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Creative elements: network-based predictions of active centres in proteins and cellular and social networks

(2008) P CSERMELY   TRENDS IN BIOCHEMICAL SCIENCES

Insights into Protein–DNA Interactions through Structure Network Analysis

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