ArticleNucleic acids research2025
Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
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- Engineering of a Nucleoside 2'-Deoxyribosyltransferase for Efficient Catalysis of 5-Halogenated-2'-Deoxypyrimidine Nucleosides via Active-Site Channel Expansion.Applied biochemistry and biotechnology · 2026Article
- Substrate scope of ancestral versus modern family-1 glycosidases.Protein science : a publication of the Protein Society · 2026Article
- Structural Prioritization of FatB Thioesterase Candidates Potentially Related to Lauric Acid-Rich Seed Oil inBiomolecules · 2026Article
- NAALADL1 modulates cellular resistance to Tumor Treating Fields in colorectal cancer.NPJ precision oncology · 2026Article
- Mol* web molecular graphics engine.Protein science : a publication of the Protein Society · 2026Article
- Engineering membrane-bound alkane monooxygenase from Marinobacter sp. for increased activity in the selective ω-hy-droxylation of linear and branched aliphatic esters.Protein science : a publication of the Protein Society · 2026Article
- Structural and Biochemical Characterization of an Atypical α-Carbonic Anhydrase from the TardigradeMolecules (Basel, Switzerland) · 2026Article
- Metabolic engineering of Corynebacterium glutamicum for high-yield de novo biosynthesis of 5-aminovaleramide, a promising bio-based monomer.Microbial cell factories · 2026Article
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Authors and funding
9 authors.
Funding
Abstract
Enzymes with buried active sites utilize molecular tunnels to exchange substrates, products, and solvent molecules with the surface. These transport mechanisms are crucial for protein function and influence various properties. As proteins are inherently dynamic, their tunnels also vary structurally. Understanding these dynamics is essential for elucidating structure-function relationships, drug discovery, and bioengineering. Caver Web 2.0 is a user-friendly web server that retains all Caver Web 1.0 functionalities while introducing key improvements: (i) generation of dynamic ensembles via automated molecular dynamics with YASARA, (ii) analysis of dynamic tunnels with CAVER 3.0, (iii) prediction of ligand trajectories in multiple snapshots with CaverDock 1.2, and (iv) customizable ligand libraries for virtual screening. Users can assess protein flexibility, identify and characterize tunnels, and predict ligand trajectories and energy profiles in both static and dynamic structures. Additionally, the platform supports virtual screening with FDA/EMA-approved drugs and user-defined datasets. Caver Web 2.0 is a versatile tool for biological research, protein engineering, and drug discovery, aiding the identification of strong inhibitors or new substrates to bind to the active sites or tunnels, and supporting drug repurposing efforts. The server is freely accessible at https://loschmidt.chemi.muni.cz/caverweb.
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