About

Proteins are fundamental building blocks of all living organisms. They perform their function by binding to other molecules. This project deals with interactions between proteins and small molecules (so called ligands) because most of the currently used drugs are small molecules. While there are several tools that can predict these interactions, they are almost none for their visualization. Thus, we built a new visualization website by combining several protein visualizers together. Since evolutionary homology correlates with binding sites, our web interface also displays homology for comparison. We developed several ways how to calculate homology, and used it to improve detection of protein-ligand binding sites. Here we present PrankWeb, a modern web application for structure and sequence visualization of a protein and its protein-ligand binding sites as well as evolutionary homology. We hope that it will provide a quick and convenient way for scientists to analyze proteins.

Underlying method

PrankWeb is web interface based on P2Rank standalone method . For batch-processing, it is recommended to download standalone version of P2Rank and run experiments locally.

Training Datasets

PrankWeb classification models have been trained and validated on publicly available datasets .

Precomputed predictions

We have computed the ligand-binding sites predictions for two components of the AlphaFold DB, the “model organism proteomes” and “Swiss-Prot”, as well as PDB. For each database, AlphaFold DB and PDB, we computed the prediction with and without conservations. What is available for download is the content of the predictions directory created as described at wiki page Large scale Predictions.

Citing

If you use P2Rank online service, please cite:

Authors

David Hoksza
(contact person)

Faculty of Mathematics and Physics, Charles University

david.hoksza (at) matfyz.cuni.cz.

Lukas Jendele

Faculty of Mathematics and Physics, Charles University

Department of Computer Science, ETH Zurich

lukas.jendele (at) gmail.com

Radoslav Krivák

Faculty of Mathematics and Physics, Charles University

rkrivak (at) gmail.com

Marian Novotný

Faculty of Science, Charles University

marian.novotny (at) natur.cuni.cz


PrankWeb is a part of services provided by ELIXIR – European research infrastructure for biological information.
See services provided by ELIXIR's Czech Republic Node.

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