ArticleNucleic acids research2021
ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Structural instability impairs function of the UDP-xylose synthase 1 Ile181Asn variant associated with short-stature genetic syndrome in humans.FEBS letters · 2026Article
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- A new view of missense mutations in α-mannosidosis using molecular dynamics conformational ensembles.Protein science : a publication of the Protein Society · 2025Article
- ASD2023: towards the integrating landscapes of allosteric knowledgebase.Nucleic acids research · 2024Article
- AlloReverse: multiscale understanding among hierarchical allosteric regulations.Nucleic acids research · 2023Article
- Enhancement of SARS-CoV-2 receptor-binding domain activity by two microbial defensins.Frontiers in microbiology · 2023Article
- Probing Mechanisms of Binding and Allostery in the SARS-CoV-2 Spike Omicron Variant Complexes with the Host Receptor: Revealing Functional Roles of the Binding Hotspots in Mediating Epistatic Effects and Communication with Allosteric Pockets.International journal of molecular sciences · 2022Article
- Allosteric Hotspots in the Main Protease of SARS-CoV-2.Journal of molecular biology · 2022Article
- Relative, local and global dimension in complex networks.Nature communications · 2022Article
- Design and engineering of allosteric communications in proteins.Current opinion in structural biology · 2022Review
- Prediction of allosteric sites and signaling: Insights from benchmarking datasets.Patterns (New York, N.Y.) · 2022Article
- Mutation-driven evolution of antibacterial function in an ancestral antifungal scaffold: Significance for peptide engineering.Frontiers in microbiology · 2022Article
- Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.Frontiers in pharmacology · 2022Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The investigation of allosteric effects in biomolecular structures is of great current interest in diverse areas, from fundamental biological enquiry to drug discovery. Here we present ProteinLens, a user-friendly and interactive web application for the investigation of allosteric signalling based on atomistic graph-theoretical methods. Starting from the PDB file of a biomolecule (or a biomolecular complex) ProteinLens obtains an atomistic, energy-weighted graph description of the structure of the biomolecule, and subsequently provides a systematic analysis of allosteric signalling and communication across the structure using two computationally efficient methods: Markov Transients and bond-to-bond propensities. ProteinLens scores and ranks every bond and residue according to the speed and magnitude of the propagation of fluctuations emanating from any site of choice (e.g. the active site). The results are presented through statistical quantile scores visualised with interactive plots and adjustable 3D structure viewers, which can also be downloaded. ProteinLens thus allows the investigation of signalling in biomolecular structures of interest to aid the detection of allosteric sites and pathways. ProteinLens is implemented in Python/SQL and freely available to use at: www.proteinlens.io.
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Registered trials
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