Rigidity and flexibility of biological networks

ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality

(2012) Máté Szalay-Bekő et al.   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

Tensegrity and motor-driven effective interactions in a model cytoskeleton

(2012) Shenshen Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses

(2012) J E Jimenez-Roldan et al.   PHYSICAL BIOLOGY

Calculating Ensemble Averaged Descriptions of Protein Rigidity without Sampling

(2012) Luis C. González et al.   PLoS One

FLEXIBLE AND ROBUST NETWORKS

(2012) SERGEY A. VAKULENKO et al.   Journal of Bioinformatics and Computational Biology

STRUCTURE FLUCTUATIONS AND CONFORMATIONAL CHANGES IN PROTEIN BINDING

(2012) ANATOLY M. RUVINSKY et al.   Journal of Bioinformatics and Computational Biology

Characterizing protein motions from structure

(2011) Charles C. David et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM maps

(2011) Arun Prasad Pandurangan et al.   JOURNAL OF STRUCTURAL BIOLOGY

KINARI-Web: a server for protein rigidity analysis

(2011) N. Fox et al.   NUCLEIC ACIDS RESEARCH

From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact Estimation

(2011) Weitao Sun et al.   PLoS One

Learning and structure of neuronal networks

(2011) KIRAN M KOLWANKAR et al.   PRAMANA-JOURNAL OF PHYSICS

Dynamic reconfiguration of human brain networks during learning

(2011) D. S. Bassett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constraint counting on RNA and ribosomal structures: linking flexibility and function

(2011) Simone Fulle et al.   Journal of Cheminformatics

Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation

(2011) Ágoston Mihalik et al.   PLoS Computational Biology

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

(2010) MS Vijayabaskar et al.   BMC BIOINFORMATICS

Hematopoietic differentiation: a coordinated dynamical process towards attractor stable states

(2010) Nadia Felli et al.   BMC Systems Biology

Correlating allostery with rigidity

(2010) A. J. Rader et al.   Molecular BioSystems

Rhythmogenic neuronal networks, emergent leaders, andk-cores

(2010) David J. Schwab et al.   PHYSICAL REVIEW E

Community Landscapes: An Integrative Approach to Determine Overlapping Network Module Hierarchy, Identify Key Nodes and Predict Network Dynamics

(2010) István A. Kovács et al.   PLoS One

Protein rigidity and thermophilic adaptation

(2010) Sebastian Radestock et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework

(2010) Pavel I. Zhuravlev et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

Coarse-Grained Description of Protein Internal Dynamics: An Optimal Strategy for Decomposing Proteins in Rigid Subunits

(2009) R. Potestio et al.   BIOPHYSICAL JOURNAL

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells

(2009) Mike J Mason et al.   BMC GENOMICS

The structural basis of allosteric regulation in proteins

(2009) Roman A. Laskowski et al.   FEBS LETTERS

Genome-wide system analysis reveals stable yet flexible network dynamics in yeast

(2009) M. Gustafsson et al.   IET Systems Biology

Statics of the Ribosomal Exit Tunnel: Implications for Cotranslational Peptide Folding, Elongation Regulation, and Antibiotics Binding

(2009) Simone Fulle et al.   JOURNAL OF MOLECULAR BIOLOGY

Probing Conformational Plasticity of the Activation Domain of Trypsin:  The Role of Glycine Hinges†

(2008) Linda Gombos et al.   BIOCHEMISTRY

Analyzing the Flexibility of RNA Structures by Constraint Counting

(2008) Simone Fulle et al.   BIOPHYSICAL JOURNAL

Proteins As Networks: Usefulness of Graph Theory in Protein Science

(2008) Alessandro Giuliani et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

A multi-modular tensegrity model of an actin stress fiber

(2008) Yaozhi Luo et al.   JOURNAL OF BIOMECHANICS

Collective motions of rigid fragments in protein structures from smoothed electron density distributions

(2008) Laurence Leherte et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Cooperativity and biological complexity

(2008) Adrian Whitty   Nature Chemical Biology

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Tensegrity-based mechanosensing from macro to micro

(2008) Donald E. Ingber   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Principles of flexible protein-protein docking

(2008) Nelly Andrusier et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of NMR order parameters in proteins using weighted protein contact-number model

(2008) Shao-Wei Huang et al.   THEORETICAL CHEMISTRY ACCOUNTS

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

(2008) P CSERMELY   TRENDS IN BIOCHEMICAL SCIENCES