ArticleProtein science : a publication of the Protein Society2013
An automated approach to network features of protein structure ensembles.
Article in Protein science : a publication of the Protein Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
- DRUMBEAT temporally resolved interpretable machine learning model for characterizing state transitions in protein dynamics.Communications biology · 2026Article
- Allostery between Distant Structural Regions Dictates Selectivity in GPCR:G Protein Coupling.Biochemistry · 2026Article
- Using Total Network Dissimilarity to Analyze Protein Structures Across Homologs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Elucidating HER2-directed chimeric antigen receptor (CAR) activation mechanism using homology modeling and all-atom molecular dynamics simulation.Computational and structural biotechnology journal · 2026Article
- A comprehensive review on structural insights through molecular visualization: tools, applications, and limitations.Journal of molecular modeling · 2025Review
- BaNDyT: Bayesian Network modeling of molecular Dynamics Trajectories.bioRxiv : the preprint server for biology · 2024Article
- Amino-Acid Characteristics in Protein Native State Structures.Biomolecules · 2024Article
- Protein Function Analysis through Machine Learning.Biomolecules · 2022Review
- Understanding structural variability in proteins using protein structural networks.Current research in structural biology · 2022Article
- SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations.PloS one · 2022Article
- Mechanistic insight into the impact of a bivalent ligand on the structure and dynamics of a GPCR oligomer.Computational and structural biotechnology journal · 2022Article
- PSNtools for standalone and web-based structure network analyses of conformational ensembles.Computational and structural biotechnology journal · 2022Article
- The Bio3D packages for structural bioinformatics.Protein science : a publication of the Protein Society · 2021Article
- Article
- Network Re-Wiring During Allostery and Protein-Protein Interactions: A Graph Spectral Approach.Methods in molecular biology (Clifton, N.J.) · 2021Review
- webPSN v2.0: a webserver to infer fingerprints of structural communication in biomacromolecules.Nucleic acids research · 2020Article
- Surveying the Side-Chain Network Approach to Protein Structure and Dynamics: The SARS-CoV-2 Spike Protein as an Illustrative Case.Frontiers in molecular biosciences · 2020Review
- NAPS update: network analysis of molecular dynamics data and protein-nucleic acid complexes.Nucleic acids research · 2019Article
- ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism.Nucleic acids research · 2019Article
- "Infostery" analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations.Scientific reports · 2018Article
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3 authors.
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Abstract
Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of β2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.
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