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%3A00082436" target="_blank" >RIV/00159816:_____/25:00082436 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14310/25:00141546

Result on the web

<a href="https://academic.oup.com/nar/article/53/W1/W132/8126903" target="_blank" >https://academic.oup.com/nar/article/53/W1/W132/8126903</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gkaf399" target="_blank" >10.1093/nar/gkaf399</a>

Result language

angličtina

Original language name

Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins

Original language description

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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

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

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

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

Publication year

2025

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

1362-4962

Volume of the periodical

53

Issue of the periodical within the volume

W1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

11

Pages from-to

"W132"-"W142"

UT code for WoS article

001483475700001

EID of the result in the Scopus database

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