ReviewComputational and structural biotechnology journal2013
Small world network strategies for studying protein structures and binding.
Review in Computational and structural biotechnology journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed, 55 citations in OpenAlex.
- Untangling the Complexity of Binding Across Biomolecular Interfaces with Interaction Network Models.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Temperature induces a shift from insulin dihexamer to hexamer in collective dynamics.Protein science : a publication of the Protein Society · 2025Article
- Heterogeneous network approaches to protein pathway prediction.Computational and structural biotechnology journal · 2024Review
- Reviewing the Structure-Function Paradigm in Polyglutamine Disorders: A Synergistic Perspective on Theoretical and Experimental Approaches.International journal of molecular sciences · 2024Review
- SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations.PloS one · 2022Article
- Understanding structural variability in proteins using protein structural networks.Current research in structural biology · 2022Article
- Saturation Mutagenesis of the Transmembrane Region of HokC inInternational journal of molecular sciences · 2021Article
- Exploring the conformational dynamics and flexibility of intrinsically disordered HIV-1 Nef protein using molecular dynamic network approaches.3 Biotech · 2021Article
- Protein conformational switch discerned via network centrality properties.Computational and structural biotechnology journal · 2021Article
- pyProGA-A PyMOL plugin for protein residue network analysis.PloS one · 2021Article
- Increasing the Affinity of an O-Antigen Polysaccharide Binding Site in Shigella flexneri Bacteriophage Sf6 Tailspike Protein.Chemistry (Weinheim an der Bergstrasse, Germany) · 2020Article
- RBinds: A user-friendly server for RNA binding site prediction.Computational and structural biotechnology journal · 2020Article
- Investigating Phosphorylation-Induced Conformational Changes in WNK1 Kinase by Molecular Dynamics Simulations.ACS omega · 2019Article
- ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism.Nucleic acids research · 2019Article
- NAPS update: network analysis of molecular dynamics data and protein-nucleic acid complexes.Nucleic acids research · 2019Article
- Building Bridges Between Structural and Network-Based Systems Biology.Molecular biotechnology · 2019Review
- gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.Nucleic acids research · 2018Article
- Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.Journal of molecular modeling · 2016Article
- NAPS: Network Analysis of Protein Structures.Nucleic acids research · 2016Article
- Weighted protein residue networks based on joint recurrences between residues.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small world network concepts provide many new opportunities to investigate the complex three dimensional structures of protein molecules. This mini-review explores the published literature on using small-world network approaches to study protein structure, with emphasis on the different combinations of descriptors that have been tested, on studies involving ligand binding in protein-ligand complexes, and on protein-protein complexes. The benefits and success of small world network approaches, which change the focus from specific interactions to the local environment, even to non-local phenomenon, are described. The purpose is to show the different ways that small world network concepts have been used for building new computational models for studying protein structure and function, and for extending and improving existing modelling approaches.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.