Issues

• Replace nextflow components with Metaflow

  AltinLab/af3-linear-epitopes#30 · Filter by author ljwoods2 opened on Jul 23, 2025

• Save AF3 embeddings for existing datasets (for use in FFN)

  AltinLab/af3-linear-epitopes#29 · Filter by author ljwoods2 opened on Jul 11, 2025

• Change RSA probe size to reflect real antibody chain

  AltinLab/af3-linear-epitopes#28 · Filter by author ljwoods2 opened on Jul 9, 2025

• HV1 segmentation inference

  AltinLab/af3-linear-epitopes#27 · Filter by author ljwoods2 opened on Jul 9, 2025
  

• Sanity check: reproducing BP3 scoring

  AltinLab/af3-linear-epitopes#26 · Filter by author ljwoods2 opened on Jul 7, 2025

• 30mer inference RMSD vs 30mer window in focal protein inference

  AltinLab/af3-linear-epitopes#25 · Filter by author ljwoods2 opened on Jul 3, 2025

• Write a github action that runs all data cleaning scripts

  AltinLab/af3-linear-epitopes#23 · Filter by author ljwoods2 opened on Jul 2, 2025

• Double-threshold HV1 in the same way as IN1

  AltinLab/af3-linear-epitopes#18 · Filter by author ljwoods2 opened on Jun 25, 2025
  

• Stretch goal: Attempt to identify 30mers from focal proteins alone using segmentation

  AltinLab/af3-linear-epitopes#14 · Filter by author ljwoods2 opened on Jun 24, 2025

• Stretch goal: modify bepipred 3.0 with structural information

  AltinLab/af3-linear-epitopes#13 · Filter by author ljwoods2 opened on Jun 24, 2025

• Evaluate AF3 best methods on BP3C50ID (bepipred train/test set)

  AltinLab/af3-linear-epitopes#10 · Filter by author ljwoods2 opened on Jun 24, 2025