google-deepmind/alphafold3

Issues

• ValueError: AlphaFold 3 input JSON has unsupported version: 2, expected 1

  #193 opened 15 days ago by HUST6324
  6

• TypeError: DataPipelineConfig.__init__() got an unexpected keyword argument 'max_template_date'

  #203 opened 12 days ago by casta126
  1

• Unclear installation instruction

  #201 opened 13 days ago by hofmank0
  7

• Permission problems when creating the output directory

  #157 opened 13 days ago by hezhiqiang8909
  7

• Can I initialize the model network with random parameters before I request the official ckpt file?

  #199 opened 14 days ago by Fx-Ren
  3

• Running on CUDA 12.2

  #202 opened 13 days ago by Jameel9
  1

• userCCD input issue

  #198 opened 14 days ago by xuewuzhang-UTSW
  3

• Typo in Input format guide

  #190 opened 14 days ago by rachelse
  1

• Broken C-Br (or C-Cl) bond within ligands

  #163 opened 14 days ago by taiyocching
  5

• Orienting membrane bound proteins

  #191 opened 15 days ago by OrangeyO2
  2

• How to compute pdockq and dockq from af3 outputs?

  #196 opened 14 days ago by wenhuihuang19791109
  1

• how come it produces so different ipTM scores when I ran the prediction three times

  #197 opened 14 days ago by HanLab-OSU
  1

• Covalent ligands: (non)leaving atoms and unrealistic bond lengths

  #159 opened 15 days ago by alephreish
  16

• Conversion to CCD CIF

  #178 opened 17 days ago by YoavShamir5
  5

• No response after multiple submissions for weights access

  #185 opened 16 days ago by swim-he
  3

• crosslinking add on to alphafold3

  #194 opened 15 days ago by fglaser
  2

• Error occurred when modeling post-translational modification

  #192 opened 15 days ago by hqdream
  1

• Bond order information missing in output cif files.

  #189 opened 16 days ago by alchemistcai
  1

• Discussion: JSON format with MSA and template features troublesome in practice

  #148 opened 20 days ago by jkosinski
  10

• can anyone provide a json template for multimer prediction input?

  #187 opened 17 days ago by drzhoufu
  1

• For several protein-protein complexes, do we need to run MSA for each complexe or can we run it first on each single proteins?

  #186 opened 17 days ago by GXcells
  1

• INTERNAL: CUDA error: Failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected

  #181 opened 17 days ago by FlypigW
  4

• GPU Memory Overflow During Sequential Complex Inference

  #165 opened 17 days ago by abiadak
  4

• Enabling explicit modeling of crosslinks: announcement and a question

  #182 opened 17 days ago by jkosinski
  2

• installing with conda, encountered compatibility issues.

  #166 opened 17 days ago by pdxooo
  3

• Template diversity

  #183 opened 18 days ago by alephreish
  1

• Is it possible to include data json file in Alphafold Server?

  #168 opened 18 days ago by sky1ove
  1

• Whether possible to add a installation version without Docker?

  #174 opened 19 days ago by paperplane03
  2

• create multimer json input by merging AF3 monomer output jsons

  #171 opened 19 days ago by James-lin9
  6

• Question regarding setting the RAM disk for MSA compute

  #176 opened 18 days ago by sky1ove
  2

• Run templates does not work with external MSA

  #169 opened 18 days ago by sky1ove
  8

• Is there a way to update the pdb database and would that be useful?

  #175 opened 18 days ago by apelin20
  1

• example of custom templates

  #167 opened 19 days ago by ShuhaoGithub
  2

• tarfile.ReadError: unexpected end of data

  #173 opened 19 days ago by koicarp98
  1

• Error about libtpu.so and module 'jaxlib.xla_extension'

  #172 opened 19 days ago by ShiDeng7rz
  1

• Where should chemical_component_sets.pickle be obtained ？

  #170 opened 19 days ago by ShiDeng7rz
  2

• corresponding chains in confidence scores

  #150 opened 19 days ago by zoeyxyang
  1

• Whether AF3 can run in CUDA-11 environment?

  #160 opened 20 days ago by Fx-Ren
  1

• ValueError: Unexpected JSON keys in: ligand

  #161 opened 20 days ago by GUMI-QXP
  3

• Feature Request: Improve MSA Generation Efficiency in AlphaFold3 with Parallelization and Queue Service

  #158 opened 21 days ago by abiadak
  1

• Inference becomes slow when input_dir have more files

  #155 opened 21 days ago by sky1ove
  2

• How does AlphaFold3 modify the number of CPU cores it runs on by passing variables? I run it through docker and submit it on an HPC cluster

  #156 opened 21 days ago by hezhiqiang8909
  2

• Cannot skip running the data pipeline

  #151 opened 22 days ago by RossoneriZhao
  3

• Can AlphaFold3 Run on the machine only with CPU and without any GPUs?

  #153 opened 21 days ago by zhaoqichang
  1

• AF3 unable to predict covalent bonds between DNA and protein

  #152 opened 22 days ago by alchemistcai
  1

• Anyway to skip predicting if the output directory already have the same name predicted file?

  #154 opened 21 days ago by sky1ove
  1

• The directory with mmcif_files has abnormal permissions and cannot be read

  #146 opened 23 days ago by hezhiqiang8909
  2

• "unpairedMsa" and "pairedMsa" fields setting of protein.

  #149 opened 24 days ago by alchemistcai
  2

• Why af3 doesn't have pickle files for multimer prediction?

  #147 opened 24 days ago by wenhuihuang19791109
  2

• Errors： downloading databases meet "/*stdin*\ : Decoding error (36) : Corrupted block detected"

  #145 opened 24 days ago by shiokoo
  1