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Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set o To build dockable name-XXXXXX.db2.gz files.

/nfs/exc/zinc22/psql-backups - TIN database backups | exc || 275 TB / 275 TB || zinc22 dockable

We back up cluster home directories daily, and selected database, crystallography and other archived files quarterly. We do not back up /nfs ...e || /nfs/home/<userid> || 500 GB || Near-daily || General use - not large database and not docking runs.

awk-scripts - bits of code for testing the database / atomtyp.txt hierstat - dockable database statistics

==Automated Docking Database Tools== #[[#Automatic Database Generation]]: You want to generate DOCK 3.5 hierarchy databases for your mo

* help you create a custom dockable database to test the fix

* [[Ligand preparation 3.7]] - Create dockable databases for [[DOCK 3.7]]. * [[Mol2db2 Format 2]] - details on the database formate.

...[[UCSF]] [[DOCK 3]] as a [[docking engine]], and [[ZINC]] as a [[dockable database]]. It runs entirely on the [[About our cluster | computer cluster ]] in the DOCK Blaster uses the same docking technology (DOCK 3) and database technology (ZINC) as is used in the Shoichet Lab for all their ([http://sho

...g the '''System Builder''' tool. Use residue information obtained from OPM database (https://opm.phar.umich.edu/), add salts, add solvent. Default settings wor ...or a mol2 file. Use the '''LigPrep''' tool to build the ligands into a 3D dockable format. Consider generating a good amount of stereoisomers if you are unsur

Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set o To build dockable name-XXXXXX.db2.gz files.

* You can provide http(s) URLs to dockable files as your input in lieu of file paths! 3a. Get db2 database subset sample via ZINC-22. Example provided below:

In INDOCK, set number_save to 50000 or something high enough to capture all dockable hierarchies. DOCK output is now gzipped so this is cheaper in disk space th ...ctation value is 0%. <y> is always "% ligands found", and <x> is either "% database searched" for enrichment plots or "% non-ligands found" for ROC plots.

# this gets the database from the autodude webpage This python script will download the dockable db2 databases from the autodude webpage.

# this gets the database from the autodude webpage This python script will download the dockable db2 databases from the autodude webpage.