Issues

• Remove redundant module inputs

  Australian-Structural-Biology-Computing/proteinfold#53 · Filter by author jscgh opened on Sep 22, 2026

• Compression of a metric-complete modelCIF?

  question
  Task

  Australian-Structural-Biology-Computing/proteinfold#44 · Filter by author keiran-rowell-unsw opened on Apr 14, 2026

• Decide on on which metrics in modelCIF or linked to it

  enhancement
  Task

  Australian-Structural-Biology-Computing/proteinfold#43 · Filter by author keiran-rowell-unsw opened on Apr 14, 2026

• Standardise metric file identifies

  enhancement
  Task

  Australian-Structural-Biology-Computing/proteinfold#42 · Filter by author keiran-rowell-unsw opened on Apr 14, 2026

• Create an ASSEMBLE_MODELCIF() process

  enhancement
  Feature

  Australian-Structural-Biology-Computing/proteinfold#41 · Filter by author keiran-rowell-unsw opened on Apr 14, 2026

• Populate modelCIF software and protocol classes

  enhancement
  Feature

  Australian-Structural-Biology-Computing/proteinfold#40 · Filter by author keiran-rowell-unsw opened on Apr 14, 2026

• Populate modelCIF metrics classes

  enhancement
  Feature

  Australian-Structural-Biology-Computing/proteinfold#39 · Filter by author keiran-rowell-unsw opened on Apr 14, 2026

• Learn from AlphaFast's parallel MSA processing

  Australian-Structural-Biology-Computing/proteinfold#38 · Filter by author keiran-rowell-unsw opened on Feb 20, 2026
  

• Benchmark against sequnece counts for weird organisms

  Australian-Structural-Biology-Computing/proteinfold#36 · Filter by author keiran-rowell-unsw opened on Feb 19, 2026

• Build benchmark dataset of unique proteins

  Australian-Structural-Biology-Computing/proteinfold#35 · Filter by author keiran-rowell-unsw opened on Feb 19, 2026
  1

• Boltzpulldown - what MSA sensitivity is acceptable for false negative rate

  Australian-Structural-Biology-Computing/proteinfold#34 · Filter by author keiran-rowell-unsw opened on Feb 19, 2026
  1

• Benchmark sensitivty tradeoff of ungapped GPU

  Australian-Structural-Biology-Computing/proteinfold#33 · Filter by author keiran-rowell-unsw opened on Feb 19, 2026
  1

• SPIRE as a new DB -- indexed

  Australian-Structural-Biology-Computing/proteinfold#32 · Filter by author keiran-rowell-unsw opened on Feb 19, 2026
  2

  

• Colabfold setup_databases for GPU and other settings a proteinfold pre-script

  Australian-Structural-Biology-Computing/proteinfold#31 · Filter by author keiran-rowell-unsw opened on Feb 19, 2026
  1

• Implement Tom's msa.nf batching draft as core pipeline function

  Australian-Structural-Biology-Computing/proteinfold#30 · Filter by author keiran-rowell-unsw opened on Feb 19, 2026

• Add documentation for create right-sized databases upon instutional admin install

  enhancement
  Australian-Structural-Biology-Computing/proteinfold#26 · Filter by author keiran-rowell-unsw opened on Jan 29, 2026
  3

• Config variables for insitutes to set GPU acceleration

  enhancement
  Australian-Structural-Biology-Computing/proteinfold#22 · Filter by author keiran-rowell-unsw opened on Jan 29, 2026
  9

  

• --db-load-mode 2 for single sequence queries

  enhancement
  Australian-Structural-Biology-Computing/proteinfold#21 · Filter by author keiran-rowell-unsw opened on Jan 29, 2026
  1

  

• Obsolete.dat template mapping causes errors

  bug
  Bug

  Australian-Structural-Biology-Computing/proteinfold#20 · Filter by author jscgh opened on Aug 20, 2025

• Interaction screening - one-to-all, pairwise multimer predictions

  enhancement
  Feature

  Australian-Structural-Biology-Computing/proteinfold#14 · Filter by author keiran-rowell-unsw opened on Feb 10, 2025 · Protein interaction screening

• Write flow documentation guiding which mode to use for use-case

  documentation
  Feature

  Australian-Structural-Biology-Computing/proteinfold#12 · Filter by author jscgh opened on Feb 10, 2025 · Easy 'self-service' of proteinfold web interface

• Benchmark Chai-1 against Boltz-1

  good first issuequestion
  Task

  Australian-Structural-Biology-Computing/proteinfold#11 · Filter by author jscgh opened on Feb 10, 2025 · Highly efficient AlphaFold3 reimplementation (Boltz + MMSeq-GPU)