The First CACHE Challenge – Testing Diverse Virtual Screening Scoring Methods to Identify Potential LRRK2 Binders

07 March 2024, Version 3
This content is a preprint and has not undergone peer review at the time of posting.

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.

Keywords

CACHE
Drug Discovery
CADD
Fitted
Structure-based drug design

Supplementary materials

Title
Description
Actions
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
Actions
Title
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
Actions

Supplementary weblinks

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.