Analysis of core-periphery organization in protein contact networks reveals groups of structurally and functionally critical residues (Q86693817)

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29 February 2020

title

Analysis of core-periphery organization in protein contact networks reveals groups of structurally and functionally critical residues (English)

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29 February 2020

author name string

Arnold Emerson Isaac

series ordinal

1

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29 February 2020

Sitabhra Sinha

series ordinal

2

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29 February 2020

publication date

1 October 2015

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29 February 2020

published in

Journal of Biosciences

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29 February 2020

volume

40

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29 February 2020

issue

4

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29 February 2020

page(s)

683-699

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ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

29 February 2020

cites work

1 reference

12 December 2020

Protein contact networks: an emerging paradigm in chemistry

1 reference

12 December 2020

Modules identification in protein structures: the topological and geometrical solutions.

1 reference

12 December 2020

Insights into the quaternary association of proteins through structure graphs: a case study of lectins

1 reference

12 December 2020

Understanding the mind of a worm: hierarchical network structure underlying nervous system function in C. elegans

1 reference

12 December 2020

Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding

1 reference

12 December 2020

Peeling the yeast protein network

1 reference

12 December 2020

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

1 reference

12 December 2020

Scanning malleable transition state ensembles: comparing theory and experiment for folding protein U1A.

1 reference

12 December 2020

From snapshot to movie: phi analysis of protein folding transition states taken one step further

1 reference

12 December 2020

A network representation of protein structures: implications for protein stability.

1 reference

12 December 2020

Experiment and theory highlight role of native state topology in SH3 folding

1 reference

12 December 2020

Intra and inter-molecular communications through protein structure network.

1 reference

12 December 2020

SRide: a server for identifying stabilizing residues in proteins

1 reference

12 December 2020

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information

1 reference

12 December 2020

Identifying the protein folding nucleus using molecular dynamics.

1 reference

12 December 2020

Small-world communication of residues and significance for protein dynamics

1 reference

12 December 2020

Specific nucleus as the transition state for protein folding: evidence from the lattice model.

1 reference

12 December 2020

Three key residues form a critical contact network in a protein folding transition state

1 reference

12 December 2020

Identification of kinetically hot residues in proteins

1 reference

12 December 2020

Statistical thermodynamics of residue fluctuations in native proteins.

1 reference

12 December 2020

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain

1 reference

12 December 2020

Slow protein evolutionary rates are dictated by surface–core association

1 reference

12 December 2020

Interaction energy based protein structure networks

1 reference

12 December 2020

Automated analysis of interatomic contacts in proteins

1 reference

12 December 2020

Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications

1 reference

12 December 2020

A simple shape characteristic of protein-protein recognition.

1 reference

12 December 2020

Lethality and centrality in protein networks

1 reference

12 December 2020

Uncovering network systems within protein structures.

1 reference

12 December 2020

Satisfying turns in folding transitions

1 reference

12 December 2020

Association of putative concave protein-binding sites with the fluctuation behavior of residues

1 reference

12 December 2020

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

1 reference

12 December 2020

An evolutionary trace method defines binding surfaces common to protein families

1 reference

12 December 2020

Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families

1 reference

12 December 2020

Residues crucial for maintaining short paths in network communication mediate signaling in proteins

1 reference

12 December 2020

Nucleation mechanisms in protein folding

1 reference

12 December 2020

Residue interaction network analysis of Dronpa and a DNA clamp.

1 reference

12 December 2020

Identifying folding nucleus based on residue contact networks of proteins

1 reference

12 December 2020

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins

1 reference

12 December 2020

1 reference

12 December 2020

Protein regulation: the statistical theory of allostery

1 reference

12 December 2020

Core-periphery organization of complex networks

1 reference

12 December 2020

Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations

1 reference

12 December 2020

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

1 reference

12 December 2020

The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding

1 reference

12 December 2020

Assortative mixing in Protein Contact Networks and protein folding kinetics

1 reference

12 December 2020

Pathways for protein folding: is a new view needed?

1 reference

12 December 2020

Effects of disulfide bonds on folding behavior and mechanism of the beta-sheet protein tendamistat.

1 reference

12 December 2020

Reducing the computational complexity of protein folding via fragment folding and assembly

1 reference

12 December 2020

Simulation, experiment, and evolution: understanding nucleation in protein S6 folding

1 reference

12 December 2020

Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture

1 reference

12 December 2020

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review

1 reference

12 December 2020

Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking.

1 reference

12 December 2020

A model of Internet topology using k-shell decomposition

1 reference

12 December 2020

Random network behaviour of protein structures

1 reference

12 December 2020

Network Analysis of Protein Structures Identifies Functional Residues

1 reference

12 December 2020

Small-world network approach to identify key residues in protein-protein interaction

1 reference

12 December 2020

SIFT: Predicting amino acid changes that affect protein function

1 reference

12 December 2020

Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model

1 reference

12 December 2020

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

1 reference

12 December 2020

Collective dynamics of 'small-world' networks

1 reference

12 December 2020

THEMATICS: a simple computational predictor of enzyme function from structure

1 reference

12 December 2020

Small-world view of the amino acids that play a key role in protein folding.

1 reference

12 December 2020

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

1 reference

12 December 2020

Essential core of protein-protein interaction network in Escherichia coli

1 reference

12 December 2020

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

1 reference

12 December 2020