[en] BACKGROUND: CRISPR-Cas-Docker is a web server for in silico docking experiments with CRISPR RNAs (crRNAs) and Cas proteins. This web server aims at providing experimentalists with the optimal crRNA-Cas pair predicted computationally when prokaryotic genomes have multiple CRISPR arrays and Cas systems, as frequently observed in metagenomic data.
RESULTS: CRISPR-Cas-Docker provides two methods to predict the optimal Cas protein given a particular crRNA sequence: a structure-based method (in silico docking) and a sequence-based method (machine learning classification). For the structure-based method, users can either provide experimentally determined 3D structures of these macromolecules or use an integrated pipeline to generate 3D-predicted structures for in silico docking experiments.
CONCLUSION: CRISPR-Cas-Docker addresses the need of the CRISPR-Cas community to predict RNA-protein interactions in silico by optimizing multiple stages of computation and evaluation, specifically for CRISPR-Cas systems. CRISPR-Cas-Docker is available at www.crisprcasdocker.org as a web server, and at https://github.com/hshimlab/CRISPR-Cas-Docker as an open-source tool.
Disciplines :
Computer science Biotechnology
Author, co-author :
Park, Ho-Min ; Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea ; Department of Electronics and Information Systems, Ghent University, 9000, Ghent, Belgium
Won, Jongbum; Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea
Park, Yunseol ; Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea
Anzaku, Esla Timothy; Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea ; Department of Electronics and Information Systems, Ghent University, 9000, Ghent, Belgium
Vankerschaver, Joris ; Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea ; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000, Ghent, Belgium
Van Messem, Arnout ; Université de Liège - ULiège > Département de mathématique > Statistique appliquée aux sciences
De Neve, Wesley ; Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea ; Department of Electronics and Information Systems, Ghent University, 9000, Ghent, Belgium
Shim, Hyunjin ; Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, 21985, South Korea. hyunjin.shim@ghent.ac.kr
Language :
English
Title :
CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins.
