Sd file is same as sdf file?
sdf file from ZINC is correct or I have to alter it somehow? Its more like questions, but I think tutorial has to say something about file that is used.
again, docking in 3 steps tutorial assumes the user has previous knowledge on issues non-related to rDock itself (such as preparing an sd/sdf file with corresponding tools) and provides an easy way to run your first docking.
Moreover, rDock paper provides detailed information about how to prepare ligands, for instance.
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Hi Sergio,
I'm trying to use your DUD list and tutorial to make the ROC curve highlighted here: http://rdock.sourceforge.net/how-to-calculate-roc-curves/
I'm using the DUD collection /hivpr files from the .gz file here: http://rdock.sourceforge.net/validation-sets/#DUD
I've figured out that the .sdf.gz file contains BOTH the ligands and decoys, which makes sense given the R code. But what I don't see is the ligands.txt and decoys.txt files that one needs to code each ligand as active or decoy. All /xxxx diectories do not seem to have ligands.txt and decoys.txt files. Where can we get hold of those .txt files?
Thanks,
Ant
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Hi Ant,
Ligands and decoys txt files can be downloaded in the beggining of the tutorial.
These lists are extrated from the original DUD sets, so if you need these files for any other system than the one in the tutorial, I recommend you to get them from dud.docking.org. In some systems they are differentiated because ligands start with "CHEMBL" and decoys with "ZINC", but it depends on your particular case.
Best,
Sergio
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Please use the tickets properly: this information is easily available in internet and there is no need to open a ticket --> https://en.wikipedia.org/wiki/Chemical_table_file#SDF
again, docking in 3 steps tutorial assumes the user has previous knowledge on issues non-related to rDock itself (such as preparing an sd/sdf file with corresponding tools) and provides an easy way to run your first docking.
Moreover, rDock paper provides detailed information about how to prepare ligands, for instance.
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Hi Sergio,
I'm trying to use your DUD list and tutorial to make the ROC curve highlighted here:
http://rdock.sourceforge.net/how-to-calculate-roc-curves/
I'm using the DUD collection /hivpr files from the .gz file here:
http://rdock.sourceforge.net/validation-sets/#DUD
I've figured out that the .sdf.gz file contains BOTH the ligands and decoys, which makes sense given the R code. But what I don't see is the ligands.txt and decoys.txt files that one needs to code each ligand as active or decoy. All /xxxx diectories do not seem to have ligands.txt and decoys.txt files. Where can we get hold of those .txt files?
Thanks,
Ant
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Ant
Last edit: Anonymous 2017-01-17
Hi Ant,
Ligands and decoys txt files can be downloaded in the beggining of the tutorial.
These lists are extrated from the original DUD sets, so if you need these files for any other system than the one in the tutorial, I recommend you to get them from dud.docking.org. In some systems they are differentiated because ligands start with "CHEMBL" and decoys with "ZINC", but it depends on your particular case.
Best,
Sergio
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Great! Thanks Sergio.
ciao,
Ant