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

. 2025 Jul 07 ; 53 (W1) : W466-W471.

Jazyk angličtina Země Velká Británie, Anglie Médium print

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid40384566

Grantová podpora
23-07349S Czech Science Foundation
LM2018131 ELIXIR CZ Research Infrastructure
Ministry of Education

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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