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Build 3D of the actives using TLDR Build 3D of the decoys using TLDR

[[Category: Build 3D]]

* build 3D database - ZINC-22 style * variant 1: build for ZINC-22 at the 10M per job scale

Info on using ZINC-22 3D building in singularity. == how to build the singularity image ==

* build 3d, to build docking libraries

= Build [[pydock3]] Python package = * (e.g., build pip-installable wheel file using [[Python Poetry|poetry]]).

== 3D Covalent Building for Wynton == = Submitting 3D Covalent Building Jobs on BKS Cluster =

== 3D models == We build 10,000 3D molecules per day, 24/7/365.

the script is based in ~/zinc-3d-build-3 on jji@wynton The script will then submit a number of jobs to build 3D ligand data and save results in an organized fashion to the output destinat

== 3D exports == ...ches about once every two months. This is only going to get worse when we build more protomers, and there are definitely ways to make this run a lot faster

...ome of these because they were not ready to build when we had attempted to build, some because they failed, some because they got lost in processing, and so

Examples of implementation are Insight or Discovery Studio, whereby a 3D stereochemical model of the pharmacophore is derived, either from the recep ...available, it may be possible to combine information from both sources to build a better model.

== ZINC-22 3D database updates == * zinc-22j now has about 220M new 3D molecules. Growing.

This page describes checking out ZINC22 SMILES tranches for 3D building. ...checked out but not built yet (for whatever reason) we will still want to build them, not toss them out. We can mark these molecules separately.

We have built to H39. Next time (summer) we will build to H49. == More ZINC-22 3D structures for docking ==

* zinc22-3d-submit : scripts for submitting ligand building workloads to SLURM/SGE [[Building_The_3D_Pipeline_ZINC22| How to build libraries for DOCK 3.8]]

These are notes from John to Max to help guide the curation of ZINC-22 3D. Each topic has its own subject heading. * blue = 3D build running

The following tranches in 2d-15-diff were damaged. All 3D built versions of these molecules (under /zinc-22d/. and called _15.smi ) w Don't build any of these tranches in 2d-15-diff, if you have built molecules from these

Installation of the 3D pipeline is somewhat tricky- the environment is very particular about which <nowiki>git clone https://github.com/docking-org/zinc22-3d-submit</nowiki>

== 3 ways to build ligands: == 1. Source the dock environment and run the stand-alone script to build ligands for a given smiles file: