| Autor: |
Ho-min Park, Jongbum Won, Yunseol Park, Esla Timothy Anzaku, Joris Vankerschaver, Arnout Van Messem, Wesley De Neve, Hyunjin Shim |
| Rok vydání: |
2023 |
| DOI: |
10.1101/2023.01.04.522819 |
| Popis: |
MotivationCRISPR-Cas-Docker is a web server forin silicodocking 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. CRISPR-Cas-Docker provides two methods to predict the optimal Cas protein given a particular crRN sequence: a structure-based method (in silicodocking) 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 forin silicodocking experiments.ResultsCRISPR-Cas-Docker is an optimized and integrated platform that provides users with 1) 3D-predicted crRNA structures and AlphaFold-predicted Cas protein structures, 2) the top-10 docking models for a particular crRNA-Cas protein pair, and 3) machine learning-based classification of crRNA into its Cas system type.Availability and implementationCRISPR-Cas-Docker is available as an open-source tool under the GNU General Public License v3.0 on GitHub. It is also available as a web server. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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