Hackathon 2024 to consolidate the standard lab protocol

The standard lab protocol has become frayed at the edges. The purpose of this hackathon is to consolidate the multiple scripts in the lab and to arrive at a new lab protocol that captures all the best practices, tips and tricks and insider knowledge.

To begin, we enumerate the existing pages that need to be consolidated.

https://docs.google.com/document/d/1n0MBDGq7gQ6brBE4wV8WD2MJRC6ZhSn3n9pwhXAOuGc/edit#heading=h.6k8tvj60u0k3

(and references cited within)

The bender paper

https://docs.google.com/document/d/1BWSWjn3bEL3kcYL01syyXZGTs7eBZFOjHsnxPZsh4R4/edit

Elissa's protocol

https://docs.google.com/document/d/16xYvFlS1McYEd3_QfOLLsO2ukIuHRz3FNhJuh8QPzio/edit

other documents?

The protocols to be standardized are

• set up an run a molecular docking screen on Wynton
• variant 1: standard protocol (ligands and target structure(s) available)
• variant 2: target structure is not obvious, further modeling/testing required
• variant 3: flexible receptor docking
• variant 4: GIST
• variant 5: no control ligands available

• build 3D database - ZINC-22 style
• variant 1: build for ZINC-22 at the 10M per job scale
• variant 2: build up to 1000 for standalone use
• variant 3: build at the 10 million scale for standalone use

• scoreopt protocols
• grid visualization protocols

• how to setup a new computational lab protocols

• experimental lab protocols