ArticleBioMed research international2017
Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case.
Article in BioMed research international, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- PyPCN: protein contact networks in PyMOL.Bioinformatics (Oxford, England) · 2023Article
- Article
- Assembly of Biomolecular Gigastructures and Visualization with the Vulkan Graphics API.Journal of chemical information and modeling · 2021Article
- Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models.Journal of molecular liquids · 2021Article
- Drug design by machine-trained elastic networks: predicting Ser/Thr-protein kinase inhibitors' activities.Molecular diversity · 2021Article
- Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC.Molecules (Basel, Switzerland) · 2021Article
- Molecular Dynamics Simulation Techniques as Tools in Drug Discovery and Pharmacology: A Focus on Allosteric Drugs.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Identification of Allosteric Effects in Proteins by Elastic Network Models.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Disclosing Allostery Through Protein Contact Networks.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Mechanism of Action of Non-Synonymous Single Nucleotide Variations Associated withMolecules (Basel, Switzerland) · 2019Article
- ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism.Nucleic acids research · 2019Article
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4 authors.
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Abstract
The overall topology and interfacial interactions play key roles in understanding structural and functional principles of protein complexes. Elastic Network Model (ENM) and Protein Contact Network (PCN) are two widely used methods for high throughput investigation of structures and interactions within protein complexes. In this work, the comparative analysis of ENM and PCN relative to hemoglobin (Hb) was taken as case study. We examine four types of structural and dynamical paradigms, namely, conformational change between different states of Hbs, modular analysis, allosteric mechanisms studies, and interface characterization of an Hb. The comparative study shows that ENM has an advantage in studying dynamical properties and protein-protein interfaces, while PCN is better for describing protein structures quantitatively both from local and from global levels. We suggest that the integration of ENM and PCN would give a potential but powerful tool in structural systems biology.
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