AutoDock Vina Help
Hi Everyone, As of the end of April 2020, the webserver to opal is no longer working. I have tried to build the PDB2PQR programme locally but have been struggling. Basically, need to align a RNA molecule to a sight within the pdb. If anyone can help, please assist. Thank you, Ali from Cape Town
Hi Ali, There are a huge number of docking programs: Autodock Vina, UCSF DOCK and many others. However, I don't know which can be used for RNA-protein docking vs. small molecule-protein or protein-protein docking, so you may need to investigate or literature-search that yourself. I should also mention that the sampling that was allowed by the Autodock Vina web service was extremely unlikely to be sufficient for something as flexible and big as RNA, so I don't think that would have been the right tool for your question anyway. You may have gotten a result but it wouldn't be a reliable indicator of reality. <http://vina.scripps.edu/> <http://dock.compbio.ucsf.edu/> You would need to obtain and use the docking program directly (not through a Chimera interface). Then you may be able to look at the output using the ViewDock tool in Chimera. Not sure why you mentioned PDB2PQR... I don't think that has anything to do with Autodock Vina. If you want the ease of a web server (nothing to install yourself) a few are listed below. However, again I do not know if they are intended or can be used for RNA-protein docking. SwissDock <http://www.swissdock.ch/> Webina <https://durrantlab.pitt.edu/webina/> DOCK Blaster <http://blaster.docking.org/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 23, 2020, at 8:46 AM, Ali <alikiyaei@gmail.com> wrote:
Hi Everyone,
As of the end of April 2020, the webserver to opal is no longer working. I have tried to build the PDB2PQR programme locally but have been struggling.
Basically, need to align a RNA molecule to a sight within the pdb. If anyone can help, please assist.
Thank you,
Ali from Cape Town
Another useful server, especially for protein-protein and protein-nucleic acids, is Haddock. https://haddock.science.uu.nl/ It is for biomolecular complex and is based on your experimental restraints (mutations, spectroscopic data, etc.). Best Marco Il 23/06/2020 22:16, Elaine Meng ha scritto:
Hi Ali, There are a huge number of docking programs: Autodock Vina, UCSF DOCK and many others. However, I don't know which can be used for RNA-protein docking vs. small molecule-protein or protein-protein docking, so you may need to investigate or literature-search that yourself. I should also mention that the sampling that was allowed by the Autodock Vina web service was extremely unlikely to be sufficient for something as flexible and big as RNA, so I don't think that would have been the right tool for your question anyway. You may have gotten a result but it wouldn't be a reliable indicator of reality.
<http://vina.scripps.edu/> <http://dock.compbio.ucsf.edu/>
You would need to obtain and use the docking program directly (not through a Chimera interface). Then you may be able to look at the output using the ViewDock tool in Chimera. Not sure why you mentioned PDB2PQR... I don't think that has anything to do with Autodock Vina.
If you want the ease of a web server (nothing to install yourself) a few are listed below. However, again I do not know if they are intended or can be used for RNA-protein docking.
SwissDock <http://www.swissdock.ch/> Webina <https://durrantlab.pitt.edu/webina/> DOCK Blaster <http://blaster.docking.org/>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 23, 2020, at 8:46 AM, Ali <alikiyaei@gmail.com> wrote:
Hi Everyone,
As of the end of April 2020, the webserver to opal is no longer working. I have tried to build the PDB2PQR programme locally but have been struggling.
Basically, need to align a RNA molecule to a sight within the pdb. If anyone can help, please assist.
Thank you,
Ali from Cape Town
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-- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
participants (3)
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Ali -
Elaine Meng -
Marco Sette