Article (Scientific journals)
PrankWeb: a web server for ligand binding site prediction and visualization.
Jendele, Lukas; Krivak, Radoslav; Skoda, Petr et al.
2019In Nucleic Acids Research, 47 (W1), p. 345-W349
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Abstract :
[en] PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points with a high ligandability score are then clustered to form the resulting ligand binding sites. In addition, PrankWeb provides a web interface enabling users to easily carry out the prediction and visually inspect the predicted binding sites via an integrated sequence-structure view. Moreover, PrankWeb can determine sequence conservation for the input molecule and use this in both the prediction and result visualization steps. Alongside its online visualization options, PrankWeb also offers the possibility of exporting the results as a PyMOL script for offline visualization. The web frontend communicates with the server side via a REST API. In high-throughput scenarios, therefore, users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application. PrankWeb is available at http://prankweb.cz/, while the web application source code and the P2Rank method can be accessed at https://github.com/jendelel/PrankWebApp and https://github.com/rdk/p2rank, respectively.
Disciplines :
Computer science
Author, co-author :
Jendele, Lukas;  Charles University > Department of Software Engineering
Krivak, Radoslav;  Charles University > Department of Software Engineering
Skoda, Petr;  Charles University > Department of Software Engineering
Novotny, Marian;  Charles University > Department of Cell Biology
Hoksza, David ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) ; Charles University > Department of Software Engineering
External co-authors :
yes
Language :
English
Title :
PrankWeb: a web server for ligand binding site prediction and visualization.
Publication date :
2019
Journal title :
Nucleic Acids Research
ISSN :
1362-4962
Publisher :
Oxford University Press, United Kingdom
Volume :
47
Issue :
W1
Pages :
W345-W349
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
(c) The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
Available on ORBilu :
since 09 October 2019

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