Benchmark Reference & Guide

This section contains in-depth documentation on benchmark designs, scoring mechanics, custom target creation, and supporting automation scripts.

• The Seven Target Benchmarks
• Scoring Pipeline & Constraints
• Creating Custom Benchmarks
• Scripts & Automation

Summary of Topics

• The Seven Target Benchmarks: Detailed breakdown of the seven curated benchmark targets (CHK1, DPP4, ITK, PEPCK, PptT, TTK, VEGFR2), including crystal structures, resolution, ChEMBL assay IDs, and fragment definitions.

• Scoring Pipeline & Constraints: The 5-step scoring pipeline from 2D substructure filtering to 3D docking, pose RMSD validation, score normalization, and reward clipping.

• Creating Custom Benchmarks: Step-by-step protocol for adding, calibrating, and registering new target systems in mockdock.

• Scripts & Automation: Tooling for multi-seed variance calibration, large-scale benchmarking, and figure generation.