Caver Web 2.0: Analysis of Tunnels and Ligand Transport in Dynamic Ensembles of Proteins

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00159816%3A_____%2F25%3A00082507" target="_blank" >RIV/00159816:_____/25:00082507 - isvavai.cz</a>

Result on the web

<a href="https://loschmidt.chemi.muni.cz/caverweb/" target="_blank" >https://loschmidt.chemi.muni.cz/caverweb/</a>

DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Caver Web 2.0: Analysis of Tunnels and Ligand Transport in Dynamic Ensembles of Proteins

Original language description

CaverWeb 2.0 is a new version of a user-friendly web server designed for the analysis of protein tunnels and channels, as well as the study of ligand transport through these pathways. This tool utilizes the robust tunnel detection algorithm of Caver 3.02 and the docking capabilities of CaverDock 1.0 to provide a comprehensive suite of functionalities for researchers in structural biology and computational chemistry. Caver Web automatically identifies and characterizes tunnels within protein structures, providing detailed information about their geometry, topology, and potential functional significance. The tool allows users to simulate the transport of ligands through identified tunnels, generating energy profiles and trajectories that reveal the mechanistic details of ligand translocation. Newly Caver Web analyzes tunnels within molecular dynamics (MD) trajectories, providing insights into the dynamic nature of these pathways and their potential role in protein function. Moreover, by analyzing MD snapshots, Caver Web can assess the accessibility of protein binding sites, providing valuable information for drug discovery and design. The tool also enables screening user-defined libraries of compounds against identified tunnels, identifying potential drug candidates that can efficiently traverse the protein&apos;s interior.

Czech name

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Czech description

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Type

R - Software

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/LM2023055" target="_blank" >LM2023055: Czech National Infrastructure for Biological Data</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2025

Confidentiality

C - Předmět řešení projektu podléhá obchodnímu tajemství (§ 504 Občanského zákoníku), ale název projektu, cíle projektu a u ukončeného nebo zastaveného projektu zhodnocení výsledku řešení projektu (údaje P03, P04, P15, P19, P29, PN8) dodané do CEP, jsou upraveny tak, aby byly zveřejnitelné.

Internal product ID

6-SW-2025

Technical parameters

Doposud je využíváno interně k výzkumným účelům.

Economical parameters

V budoucnu je plánována nabídka potencionálním partnerům z komerční sféry.

Owner IČO

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Owner name

Fakultní nemocnice u sv. Anny v Brně; České vysoké učení technické