Hackathon 2024 to consolidate the standard lab protocol

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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