PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis
Jazyk angličtina Země Velká Británie, Anglie Médium print
Typ dokumentu časopisecké články
Grantová podpora
23-07349S
Czech Science Foundation
LM2018131
ELIXIR CZ Research Infrastructure
Ministry of Education
PubMed
40384566
PubMed Central
PMC12230715
DOI
10.1093/nar/gkaf421
PII: 8136464
Knihovny.cz E-zdroje
- MeSH
- internet MeSH
- konformace proteinů MeSH
- ligandy MeSH
- proteiny * chemie metabolismus MeSH
- simulace molekulového dockingu MeSH
- software * MeSH
- strojové učení MeSH
- uživatelské rozhraní počítače MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- ligandy MeSH
- proteiny * MeSH
Knowledge of protein-ligand binding sites (LBSs) is crucial for advancing our understanding of biology and developing practical applications in fields such as medicine or biotechnology. PrankWeb is a web server that allows users to predict LBSs from a given three-dimensional structure. It provides access to P2Rank, a state-of-the-art machine learning tool for binding site prediction. Here, we present a new version of PrankWeb enabling the development of both client- and server-side modules acting as postprocessing tasks on the predicted pockets. Furthermore, each module can be associated with a visualization module that acts on the results provided by both client- and server-side modules. This newly developed system was utilized to implement the ability to dock user-provided molecules into the predicted pockets using AutoDock Vina (server-side module) and to interactively visualize the predicted poses (visualization module). In addition to introducing a modular architecture, we revamped PrankWeb's interface to better support the modules and enhance user interaction between the 1D and 3D viewers. We introduced a new, faster P2Rank backend or user-friendly exports, including ChimeraX visualization.
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