I want to discover few compounds which can act as inhibitors for a particular protease enzyme. Because random hit and trial assays take a lot of time/money and effort, I want to virtually screen for future inhibitory drug candidates from/among herbal components.
I don't have any knowledge of bioinformatics, but can someone suggest free online software as well as a basic procedure (tutorial) by sharing file/ppt/lecturer?
Dear,
I don't think there are free databases for drug-ligand design but I hope this database useful for you, http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/.
Hi,
structure based virtual screening is tricky task, but basically what you need is a docking approach: you need the receptor structure file and a database of small molecules. Fort the first one try to search on PDB (www.rgsb.org) while for the second one try to download a compound library from a compounds provider (for example may bridge).
To perform the screening you need a suitable software like DOCK, GOLD, FlexX , ICM GLIDE, PhDOCK, Surflex, DOCK Blaster or similar.
Use all these keyword to look for appropriate tutorials but, again, virtual screening is a tricky task.
cheers
Hi,
In addition to Stefano's suggestions, I want to bring to your notice that, the constrains you mentioned (time/money) are biggest obstacles in such tasks. You have to compromise one. There are some tools (commercial, like accelry's) which can guide you through virtual screening and their support can spare you from classroom learning. Compromise time and first find the best target (numerous proteases are there on RCSB database, more than 6513 PDBs are available). Take your time in choosing one. The cocrystallized ligand and the binding site features be studied with due attention. As suggested by Stefano you can proceed with docking. Stefano has suggested some commercial software. You can try virtual screening using PyRx a good tool???? but you should be through docking protocol. So be patient and proceed in a step wise manner. You can not bypass bioinformatics tools if you want to do virtual screening...
Best of Luck...
If you know the target, DL structure from http://www.rcsb.org/, as Stefano suggested. I suppose you have structures of natural products you want to screen. Most cost-friendly way is to use AutoDOCK or Vina, as they are free of charge. Also you an find manuals for virtual screening on line.
You can use www.chemosophia.com online computations for prediction of inhibitors activity. Simply register there (registration is free) upload .sdf-files of your compounds, fill the checkboxes at the left side of filenames (left side of website), choose "Analysis and prognosis of biological activity", then "Next" button. Then choose biological activity you interested (there are more 50 kinds of bioactivity). Press "Next" button and then "Try for free" button. Resulting files will appear at the right side.
ParaDockS (http://www.paradocks.org; see also J Chem Inf Model 2010, 50 (5), pp. 879-89) is another example of freeware suitable for virtual screening approaches.
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