Issues

• Migrate direct Biopython utilities to Biotite and consolidate routine extras

  openvax/mhctools#627 · Filter by author iskandr opened on Oct 26, 2026

• Duplicate native scan inputs can produce numerically conflicting MHCflurry rows

  openvax/mhctools#626 · Filter by author iskandr opened on Oct 26, 2026

• Track pandas 3.1 indexing deprecations in the BigMHC integration

  openvax/mhctools#615 · Filter by author iskandr opened on Oct 23, 2026

• Investigate intermittent netMHCcons QEMU crash in macOS full suite

  openvax/mhctools#599 · Filter by author iskandr opened on Oct 19, 2026
  2

• Calibrate bond-level cleavage fractions from assay-matched measurements

  openvax/mhctools#587 · Filter by author iskandr opened on Oct 15, 2026

• Model lymphatic and draining-node extracellular exposure separately

  openvax/mhctools#579 · Filter by author iskandr opened on Oct 14, 2026

• Native MixMHCpred sequence-alignment reference times out during full local suite

  openvax/mhctools#547 · Filter by author iskandr opened on Oct 9, 2026
  4

• Recover released PhageScout classifier preprocessing for faithful new-sequence inference

  openvax/mhctools#521 · Filter by author iskandr opened on Oct 6, 2026
  1

• Add distinct human ELANE and PRTN3 extended-recognition evidence and independent inflammatory-protease benchmarks

  openvax/mhctools#519 · Filter by author iskandr opened on Oct 6, 2026

• Add human plasma kallikrein KLKB1 recognition evidence separately from tissue KLKs

  openvax/mhctools#518 · Filter by author iskandr opened on Oct 6, 2026

• Add assay-scoped human plasmin extended-recognition evidence without treating Lys/Arg as sufficient

  openvax/mhctools#517 · Filter by author iskandr opened on Oct 6, 2026

• Add extended human thrombin recognition rules with source-backed cooperative motifs

  openvax/mhctools#516 · Filter by author iskandr opened on Oct 6, 2026

• Add pH-scoped human legumain/AEP recognition evidence and observed cleavage sites

  openvax/mhctools#515 · Filter by author iskandr opened on Oct 6, 2026

• Add assay-scoped CatL sequence-recognition evidence from PICS/DIPPS and peptide-library measurements

  openvax/mhctools#514 · Filter by author iskandr opened on Oct 6, 2026

• Add CleaveNet MMP substrate predictions with native endpoint and assay provenance

  openvax/mhctools#476 · Filter by author iskandr opened on Sep 30, 2026
  1

• Add assay-scoped cathepsin and AEP coverage for APC cleavage assessments

  openvax/mhctools#470 · Filter by author iskandr opened on Sep 29, 2026
  2

• Remaining round-3 review nitpicks: test factory dedup, alternate --compartment CLI design

  openvax/mhctools#337 · Filter by author iskandr opened on Sep 14, 2026

• Minor: cleavage_models()/get_cleavage_model() do repeated linear work with no caching

  openvax/mhctools#336 · Filter by author iskandr opened on Sep 11, 2026

• Curate remaining intracellular peptidases and settle the THOP1 epitope-substrate disagreement

  openvax/mhctools#334 · Filter by author iskandr opened on Sep 10, 2026

• Resolve conflicting IRAP resistant-precursor sequence in Georgiadou 2010 before benchmarking

  openvax/mhctools#332 · Filter by author iskandr opened on Sep 10, 2026

• Validate organ-exposure comparisons without conflating tissue signal, intact peptide and cell-specific delivery

  openvax/mhctools#307 · Filter by author iskandr opened on Sep 9, 2026

• Assess draining-lymph-node exposure and injection-site compartments as distinct vaccine-relevant endpoints

  openvax/mhctools#306 · Filter by author iskandr opened on Sep 9, 2026

• Evaluate Wu 2025 descriptor-PBPK nanoparticle biodistribution model with explicit carrier-domain limits

  openvax/mhctools#305 · Filter by author iskandr opened on Sep 9, 2026

• Assess the DOTATATE PBPK model as a drug-specific organ-distribution reference, not transferable vaccine weights

  openvax/mhctools#304 · Filter by author iskandr opened on Sep 9, 2026

• Validate the distinction between cellular uptake, intracellular localization and productive antigen presentation

  openvax/mhctools#303 · Filter by author iskandr opened on Sep 9, 2026