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

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/00216208:11310/25:10504302 RIV/00216208:11320/25:10504302

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

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

Projekt

<a href="/cs/project/LM2018131" target="_blank" >LM2018131: Česká národní infrastruktura pro biologická data</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2025

Kód důvěrnosti údajů

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

Název periodika

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

1362-4962

Svazek periodika

53

Číslo periodika v rámci svazku

W1

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

6

Strana od-do

"W466"-"W471"

Kód UT WoS článku

001490021500001

EID výsledku v databázi Scopus

2-s2.0-105010277311