Hello everyone I want to know is there any online webserver which can be utilized for blind docking for ssDNA-ligand docking?. I have tried few protein-protein or protein-DNA compatible webservers but they are not working with DNA-Ligand system. If anyone has performed this kind of work please share. Thank you.
Hello,
http://www.scfbio-iitd.res.in/dock/dnadock.jsp
http://bioinfo3d.cs.tau.ac.il/PatchDock/
https://doi.org/10.1093/nar/gki481
https://doi.org/10.1021/acs.jcim.1c00341
https://doi.org/10.1021/acs.jchemed.7b00989
Rezvan Marjani thank you for kind suggestions. I would like to add few points for future studies.
Their is no option to submit 3D structure in iit. ... webserver
NLDock is not accessible at this point however it may be best option if available
Interestingly Patch Dock is working for blind docking of DNA and ligand (http://bioinfo3d.cs.tau.ac.il/PatchDock/php.php)
Achilles Blind Docking server at:
https://bio-hpc.ucam.edu/achilles/
In order to find more information and for discussion I suggest you to join the Structural Bioinformatics and High Performance Computing (BIO-HPC) discord server at:
https://discord.gg/fZyNYTsT7k
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