Hey guys this question is probably lacking appropriate detail, but forgive me as I am new to the problem. I have been asked to identify computationally a list of potential inhibitors to test for a particular protein. I have a protein structure with a substrate bound. I got a trial version of MOlsoft VLS software but the academic license is more than 5000 dollars and I simply can't afford it. Is there a way to do the same sort of thing (Virtual ligand screening ) that is accurate and has good literature use but would also be very cheap or free even? Any suggestions of softwares or things I should read would be greatly appreciated. Again my goal is to find a list of compounds that bind to my protein of interest, potentially inhibiting it.
Thanks for your time
7 answers
Cresset's software for ligand-based virtual screening is excellent:
http://www.cresset-group.com/our-customers/academic-researchers/
OpenEye's software is also widely used:
http://www.eyesopen.com/academic-request
Both have free licenses for some academic settings.
The website click2drug.org has a good list of software related to screening, docking, molecular modeling and other related topics. Here are a few of the freely available ones that I've seen used:
AnchorQuery is a cool (free) webservice developed by a lab in my department that is also worth checking out.
I have used autodock in the past for semiautomated virtual screening. We only had a few candidates, so it was not complex, but with some automation I could see it being rigged up to be mostly automated. The main part is calculating fitness, which we did by looking at interatomic distances to known residues in the active site. Our molecule was a small peptide, so these results were easy to sort through.
I could see building a database and automating it.
It also appears they have a new version, Vina. Haven't used it.
We used AutoDockTools, SwissPDBViewer, and PyMol to create inputs and view results.
You can always ask somebody with ICM license to help you with your project =)
I recently discovered Tamarind Bio (https://www.tamarind.bio), where you can do virtual screening using AutoDock or DiffDock. They have a free trial, and offer larger scale virtual screening as well I believe.
I recently discovered Tamarind Bio (https://www.tamarind.bio), where you can do virtual screening using AutoDock or DiffDock. They have a free trial, and offer larger scale virtual screening as well I believe.
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Related: http://biostar.stackexchange.com/questions/8520/docking-a-small-series-of-compunds-against-a-set-of-proteins-using-perl/8550#8550
@Michael: In that question the author is starting with a list of potential ligands, and you suggested Autodock. Does Autodock come with a compound database?
There is ZINC: http://zinc.docking.org/
how could we contact you regarding this?