sokrypton/ColabDesign

Issues

• Does is matter? ---- RSO notebook ERROR: 'i_pae' not found in ['seq_ent', 'plddt', 'pae', 'exp_res', 'helix']

  #186 opened 21 days ago by Samuel-gwb
  2

• The Fold Conditioning notebook seems to be broken

  #177 opened 2 months ago by ajasja
  6

• Template mode in AFcluster fails to retrieve pdb

  #185 opened 2 months ago by leonart3
  0

• I can't see prediction of cyclic peptide example

  #176 opened 2 months ago by kimdn
  6

• ColabDesign RFdiffusion FileNotFoundError

  #181 opened 3 months ago by ttessie2
  3

• mk_af_model.predict and localcolabfold

  #183 opened 3 months ago by vuhongai
  1

• asymmetric inputs for `get_con_loss` inside `_loss_binder`

  #184 opened 3 months ago by pagpires
  0

• ColabDesign license

  #180 opened 3 months ago by komatsuna-san
  4

• options for ligandmpnn in colabdesign

  #179 opened 4 months ago by ShuhaoGithub
  0

• binders designed don't binds at the hotspots of the target chain.

  #172 opened 5 months ago by rocke2020
  0

• WARNING: 'model_1_ptm' not found WARNING: 'model_2_ptm' not found

  #178 opened 6 months ago by wendi-luo
  0

• error in cyclic design notebook

  #175 opened 6 months ago by overlord1647
  0

• MMSEQ2 NCBI labels (how can we keep them)

  #174 opened 7 months ago by MishterBluesky
  0

• Can af_cyc_design generate cyclic pepitide with D-Amino acid

  #160 opened a year ago by yrq3027
  1

• Is it preferable for the "con" metric to have a smaller value during the optimization process?

  #171 opened 10 months ago by milkboylyf
  0

• af_model.predict failing

  #170 opened a year ago by baptiste-roelens
  2

• How to predict the Cyclic Peptide's structure by a given sequence

  #125 opened 2 years ago by aar-d-vark
  3

• mk_af_model: refolding a sequence of a experimental structure using said structure as a template performs miserably

  #167 opened a year ago by dandaman
  2

• converting other MPNN checkpoints for support in ColabDesign and JAX

  #165 opened a year ago by adrienchaton
  8

• why colabdesign alphafold limits on insertion code at chain

  #113 opened a year ago by rocke2020
  0

• XlaRuntimeError: FAILED_PRECONDITION: DNN library initialization failed.

  #164 opened a year ago by johnnytam100
  1

• Locally Run ColabDesign

  #162 opened a year ago by Leo-T-Zang
  0

• Is the "i_pae" score in the designability_test.py the same as pAE_interaction?

  #161 opened a year ago by SantiagoMille
  0

• Contigs messed up with partial diffusion and manual symmetry

  #158 opened a year ago by ali-j-scott
  0

• How to continue a design run?

  #157 opened a year ago by amin-sagar
  0

• Partially folding a structure using AF

  #156 opened a year ago by aravinda1879
  0

• fix_pos in af/fixbb

  #155 opened a year ago by dandaman
  2

• Do the soft iterations in pssm_semigreedy obey the bias matrix

  #153 opened a year ago by amin-sagar
  0

• where is the output file when finish the model.design_3stage() run?

  #135 opened 2 years ago by zzy221127
  1

• Is it possible to bypass the design step of AfDesign?

  #152 opened a year ago by johnnytam100
  0

• Can we see generated sequences other than final one?

  #123 opened 2 years ago by Hyunjoo-ibs
  1

• How to get PAE files when running RFdiffusion

  #145 opened 2 years ago by remybonnav
  0

• Allow to select the Complex_beta_ckpt model in RFdiffusion colab?

  #143 opened 2 years ago by remybonnav
  0

• Translate colab for RFdiffusion to a jupyter notebook?

  #144 opened 2 years ago by remybonnav
  0

• Patch fix_partial_contigs when residue numbering in PDB has a gap

  #142 opened 2 years ago by data2code
  2

• MPNN designed sequence not separated correctly with multiple targets and multiple binders

  #141 opened 2 years ago by data2code
  2

• Any plans to add af2seq to the colab design

  #140 opened 2 years ago by Lyang556
  0

• The sequence in design.fasta is different from the sequence in best.pdb

  #124 opened 2 years ago by Lyang556
  5

• atom index in af.prep.prep_pdb

  #139 opened 2 years ago by data2code
  1

• Using RFdiffusion to design a binder, with some parts of the binder fixed

  #131 opened 2 years ago by KoubaPetr
  6

• WARNING: 'model_1_ptm' not found

  #128 opened 2 years ago by DomML
  1

• Problem in designability_test.py

  #126 opened 2 years ago by suknamgoong1970
  2

• how to interpret results of 'use_templates=True' versus 'False' in partial_hallucination_rewire?

  #119 opened 2 years ago by genya
  1

• critical typo in kmeans.py (simport instead of import)

  #122 opened 2 years ago by jkosinski
  1

• Minimize sequence length while preserving some amount of structural stability.

  #120 opened 2 years ago by seyonechithrananda
  0

• OOM on AF DB proteins?

  #116 opened 2 years ago by Abhishaike
  2

• small fix required for newer numpy versions

  #115 opened 2 years ago by gieses
  0

• git clone error

  #112 opened 2 years ago by biotech70
  2

• Fix sequence at certain positions in Binder protocol

  #107 opened 2 years ago by aminsagar
  8

• How to use gpu or cuda for design binder

  #109 opened 2 years ago by cloudaner115
  1