ArticleComputational and structural biotechnology journal2022
PSNtools for standalone and web-based structure network analyses of conformational ensembles.
Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
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- Omega-3 DHA as a blank canvas: A molecular approximation to how lipid mediators modulate LGR6 in inflammation resolution.Protein science : a publication of the Protein Society · 2026Article
- Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026Review
- Computational Analysis ofACS chemical neuroscience · 2025Article
- Exploring the Allosteric Pathways of Asciminib in the Dual Inhibition of BCR-ABL1.Biomolecules · 2025Article
- How allosteric mutations control ligand binding in Lipocalin protein: odorant binding protein as a test case.Cellular and molecular life sciences : CMLS · 2025Article
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- Minute-timescale free-energy calculations reveal a pseudo-active state in the adenosine AChem · 2024Article
- Atomistic mechanism of coupling between cytosolic sensor domain and selectivity filter in TREK K2P channels.Nature communications · 2024Article
- Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families.Protein science : a publication of the Protein Society · 2024Article
- Mechanism of Mutation-Induced Effects on the Catalytic Function of TEV Protease: A Molecular Dynamics Study.Molecules (Basel, Switzerland) · 2024Article
- Conformational plasticity and allosteric communication networks explain Shelterin protein TPP1 binding to human telomerase.Communications chemistry · 2023Article
- Slc11 Synapomorphy: A Conserved 3D Framework Articulating Carrier Conformation Switch.International journal of molecular sciences · 2023Article
- Article
- Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles.Computational and structural biotechnology journal · 2023Article
- Connecting the dots: A practical evaluation of web-tools for describing protein dynamics as networks.Frontiers in bioinformatics · 2022Review
- Structural communication between the GTPase Sec4p and its activator Sec2p: Determinants of GEF activity and early deformations to nucleotide release.Computational and structural biotechnology journal · 2022Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structure graphs, in which interacting amino acids/nucleotides correspond to linked nodes, represent cutting-edge tools to investigate macromolecular function. The graph-based approach defined as Protein Structure Network (PSN) was initially implemented in the Wordom software and subsequently in the webPSN server. PSNs are computed either on a molecular dynamics (MD) trajectory (PSN-MD) or on a single structure. In the latter case, information on atomic fluctuations is inferred from the Elastic Network Model-Normal Mode Analysis (ENM-NMA) (PSN-ENM). While Wordom performs both PSN-ENM and PSN-MD analyses but without output post-processing, the webPSN server performs only single-structure PSN-EMN but assisting the user in input setup and output analysis. Here we release for the first time the standalone software PSNtools, which allows calculation and post-processing of PSN analyses carried out either on single structures or on conformational ensembles. Relevant unique and novel features of PSNtools are either comparisons of two networks or computations of consensus networks on sets of homologous/analogous macromolecular structures or conformational ensembles. Network comparisons and consensus serve to infer differences in functionally different states of the same system or network-based signatures in groups of bio-macromolecules sharing either the same functionality or the same fold. In addition to the new software, here we release also an updated version of the webPSN server, which allows performing an interactive graphical analysis of PSN-MD, following the upload of the PSNtools output. PSNtools, the auxiliary binary version of Wordom software, and the WebPSN server are freely available at http://webpsn.hpc.unimo.it/wpsn3.php.
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