Abstract
In December 2021, Molecular Forecaster (MFI) applied to participate in the inaugural CACHE Challenge. Organized by the Structural Genomics Consortium (SGC), CACHE (Critical Assessment of Computational Hit-finding Experiments) is a public–private partnership benchmarking initiative to enable the development of computational methods “to compare and improve small-molecule hit-finding algorithms through cycles of prediction and experimental testing.”
The MFI team has decided to take multiple research-focused approaches to our predictions in this first CACHE challenge, aiming to learn from our successes and failures. We are putting MFI’s team, expertise, and algorithms to the test, using them as a foundation to push the boundaries beyond our scientific and application successes to-date. We’ve also decided to double-down and share the details of our work with the community. The experimental results are now in and we have conducted a retrospective analysis in the second half of this manuscript.
Supplementary materials
Title
Supporting Protein Files
Description
- SWISS-Model structure (pdb format) after rebuilding the missing regions
- MD simulation input files (mdp, top and ndx format) for minimization, equilibration, and production
- Equilibrated protein structure (gro format)
- LRRK2MD-WD40 structure (pdb format), along with the files created by PREPARE and PROCESS
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Supporting documentation
Description
- GNN scores for evaluated compounds
- QMSF scores for evaluated compounds
- List of the 150 selected compounds with SMILES, scores (docking, GNN, QMSF, or visualization), key physico-chemical properties (MW, HBD, HBA, etc.) and method of selection
- Final list of 96 compounds for testing
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Supplementary weblinks
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Corresponding blog post
Description
An accompanying blog post on our website detailing our participation in the CACHE challenge.
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