PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F25%3A00637394" target="_blank" >RIV/61388963:_____/25:00637394 - isvavai.cz</a>
Alternative codes found
RIV/00216208:11310/25:10504302 RIV/00216208:11320/25:10504302
Result on the web
<a href="https://doi.org/10.1093/nar/gkaf421" target="_blank" >https://doi.org/10.1093/nar/gkaf421</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/nar/gkaf421" target="_blank" >10.1093/nar/gkaf421</a>

Result language
angličtina
Original language name
PrankWeb 4: a modular web server for protein-ligand binding site prediction and downstream analysis
Original language description
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.
Czech name
—
Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
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/LM2018131" target="_blank" >LM2018131: Czech National Infrastructure for Biological Data</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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