ArticleNucleic acids research2019
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Article
- i-gRINN: a next-generation web server for protein energy network analysis of heterogeneous biomolecular systems with natural language-based data exploration.Nucleic acids research · 2026Article
- CaRinDB: an integrated database of common cancer mutations and residue interaction network parameters.Bioinformatics advances · 2026Article
- Protein contact network explorer: topological analysis of protein structures.Frontiers in bioinformatics · 2026Article
- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- Contact networks in RNA: a structural bioinformatics study with a new tool.Journal of computer-aided molecular design · 2022Article
- pyProGA-A PyMOL plugin for protein residue network analysis.PloS one · 2021Article
- The Bio3D packages for structural bioinformatics.Protein science : a publication of the Protein Society · 2021Article
- Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy.Journal of computer-aided molecular design · 2020Article
- webPSN v2.0: a webserver to infer fingerprints of structural communication in biomacromolecules.Nucleic acids research · 2020Article
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3 authors.
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Abstract
ProSNEx (Protein Structure Network Explorer) is a web service for construction and analysis of Protein Structure Networks (PSNs) alongside amino acid flexibility, sequence conservation and annotation features. ProSNEx constructs a PSN by adding nodes to represent residues and edges between these nodes using user-specified interaction distance cutoffs for either carbon-alpha, carbon-beta or atom-pair contact networks. Different types of weighted networks can also be constructed by using either (i) the residue-residue interaction energies in the format returned by gRINN, resulting in a Protein Energy Network (PEN); (ii) the dynamical cross correlations from a coarse-grained Normal Mode Analysis (NMA) of the protein structure; (iii) interaction strength. Upon construction of the network, common network metrics (such as node centralities) as well as shortest paths between nodes and k-cliques are calculated. Moreover, additional features of each residue in the form of conservation scores and mutation/natural variant information are included in the analysis. By this way, tool offers an enhanced and direct comparison of network-based residue metrics with other types of biological information. ProSNEx is free and open to all users without login requirement at http://prosnex-tool.com.
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