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Commits on Mar 18, 2024

• implement initial guess

  Poko18

  committed
  27b6e3e

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Commits on Mar 16, 2024

• Add initial_guess parameter to predict_structure and run functions

  Poko18

  committed
  1403b76

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Commits on Mar 8, 2024

• Fix cf-af2 notebooks to work on TPU again

  milot-mirdita

  committed
  2dca108

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Commits on Mar 7, 2024

• Update dm-haiku to 0.0.12

  milot-mirdita

  committed
  1abdc19

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• colabfold_search: fix logger not printing anything

  milot-mirdita

  committed
  04d037c

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• colabfold_search: Ignoring existing index if MMSEQS_IGNORE_INDEX env var is set

  milot-mirdita

  committed
  09c251b

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Commits on Feb 25, 2024

• fixing esmfold api

  sokrypton

  committed
  d36504f

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Commits on Feb 24, 2024

• correct split of paired and unpaired msas for trimer or higher

  YoshitakaMo

  committed
  f1f6a57

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Commits on Feb 22, 2024

• fix renaming issue for multiple seqs in fasta format (#568)

  YoshitakaMo

  committed
  2ecbcb3

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• Merge pull request #572 from thachung/main

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  YoshitakaMo

  authored
  63a3ee2

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• Update utils.py

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  DimaMolod

  authored and

  YoshitakaMo

  committed
  3167d33

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• fix template search for csv input (#567)

  YoshitakaMo

  committed
  2bec5c7

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Commits on Feb 18, 2024

• Update AlphaFold2.ipynb

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  thachung

  authored
  651a24c

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Commits on Feb 13, 2024

• Replace mmCIF rsync FTP download with AWS CLI download from Amazon S3 PDB Snaphots (#566)

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  teodorpopescuQB

  and

  milot-mirdita

  authored
  9a8822f

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Commits on Jan 31, 2024

• Fix template search (#565)

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  PasqM

  authored
  0cf2621

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Commits on Jan 23, 2024

• suppress warnings for jax initialize backend

  YoshitakaMo

  committed
  a00ce1b

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Commits on Jan 8, 2024

• Tiny improvements to CLI (#538)

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  gieses

  authored
  941feec

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Commits on Dec 29, 2023

• ColabFold 1.5.5

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  milot-mirdita

  committed
  675f93a

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• Set 1.5.3 link to latest working notebook

  milot-mirdita

  committed
  8bb3b61

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• Fix tests and dependencies

  milot-mirdita

  committed
  d3ca84a

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Commits on Dec 28, 2023

• fixing esmfold_advanced to use pytorch2/cuda12

  sokrypton

  committed
  e14313f

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• fixing esmfold/openfold to use -std=c++17 (needed for cuda12 and pytorch 2)

  sokrypton

  committed
  740d844

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• Bug fix in models.py (#545)

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  mjag1898

  authored
  ea50984

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• ColabFold v1.5.4

  milot-mirdita

  committed
  c490e54

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• Remove sed patch for jax 0.4

  milot-mirdita

  committed
  4e9714a

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• Fix citations not correctly including alphafold

  milot-mirdita

  committed
  5fd3a84

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• Fix pae plots being generated for non ptm models

  milot-mirdita

  committed
  2515b3b

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• Add deepfold model https://academic.oup.com/bioinformatics/article/39/12/btad712/7443992

  milot-mirdita

  committed
  f80e0d8

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• Update dependencies:

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  milot-mirdita

  committed
  50e385e

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• Remove biopython 1.81 pinning and dm-haiku upgrade within colabs

  milot-mirdita

  committed
  cd18fd0

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Commits on Dec 22, 2023

• fixing biopython 1.81

  sokrypton

  committed
  56c7204

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• fixing biopython 1.81

  sokrypton

  committed
  b8d4895

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• fixing biopython 1.81

  sokrypton

  committed
  31f33cc

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Commits on Dec 18, 2023

• Add --jobname-prefix parameter for predictable filenames instead of header/accessions

  milot-mirdita

  committed
  5bb28b0

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Commits on Dec 15, 2023

• Upgrade jax to 0.4 in batch notebook too

  milot-mirdita

  committed
  ebfa87e

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