Building Covalent Libraries

Here are your instructions for building libraries for covalent docking.

Using ligands with hot functionality in screening quantities

• Search ZINC to find eligible compounds in screening quantities. See Covalent libraries for sale

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/catalog.purchasable%20eq%2050&structure%20contains%20COc1ccccc1?count=all

• Tag covalent attachment point
• Build dockable libraries from SMILES

Building libraries by reaction using building blocks in preparative quantities

• Select a reaction One step reactions for covalent ligands
• Search ZINC for building blocks in preparative quantities

http://zincapi.ucsf.bkslab.org/v1/substances/txt:smiles,zinc_id/catalog.purchasable%20eq%2050&catalog.bb%20eq%20true&structure%20contains%20COc1ccccc1?count=all

• use reactsmi.py in the DOCK 3.7 distribution to perform the reaction
• Tag covalent attachment point
• Build dockable libraries from SMILES

Tag covalent attachment point

• show how to do it here

Build dockable libraries from SMILES

• assumes you have tagged the covalent attachment point, as above
• molecules may be purchased directly, or have been created by reaction, above.

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