19 Issues closed by 2 people

• Possibility to enforce cis/trans isomer using a user-defined CCD input?

  #237 closed Jan 10, 2025

• Initial guess for multimer structure prediction

  #251 closed Jan 10, 2025

• Never received model params

  #252 closed Jan 10, 2025

• I submitted a task on https://alphafoldserver.com/, and the prediction only took two minutes. However, running it locally takes 40 minutes. Is it because the website runs without MSA search?

  #253 closed Jan 10, 2025

• Regarding incorrect covalent ligand structure

  #250 closed Jan 9, 2025

• Regarding choosing best structure and complex

  #249 closed Jan 9, 2025

• Possible Issue with RNA Chains in Paired MSA Construction

  #238 closed Jan 9, 2025

• How to run AF3 with one mmcif template file properly

  #225 closed Jan 9, 2025

• rasa calculation failed

  #55 closed Jan 9, 2025

• How to choose seeds ？

  #246 closed Jan 8, 2025

• input format for predicting protein complexes

  #248 closed Jan 8, 2025

• Documentation - chain_pair_pae_min

  #243 closed Jan 7, 2025

• How to use AlphaFold3 to predict the structure of protein-cyclic peptide complexes？

  #242 closed Jan 7, 2025

• Could you suggest how to run from shortest sequence to longest sequence?

  #241 closed Jan 7, 2025

• mol_to_ccd_cif does not set _chem_comp_atom.pdbx_leaving_atom_flag

  #233 closed Jan 6, 2025

• Something seems to be wrong in input.md

  #232 closed Jan 6, 2025

• CUDA_ERROR_OUT_OF_MEMORY issue when running test case on 4090 24G GPU machine locally

  #209 closed Jan 6, 2025

• `allow_pickle=False` not available in NumPy 2.1.3

  #235 closed Jan 6, 2025

• Inconsistent forecast accuracy

  #228 closed Jan 6, 2025

2 Issues opened by 2 people

• TypeError: unhashable type: 'list'`

  #245 opened Jan 7, 2025

• Get error in MSA process and find StopIteration error

  #244 opened Jan 7, 2025

4 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• Question: Do the terms of the open-source version allow use with automated systems?

  #239 commented on Jan 6, 2025 • 0 new comments

• `alphafold3.cpp` Module Not Found During Execution

  #234 commented on Jan 6, 2025 • 0 new comments

• RuntimeWarning: overflow encountered in reduce

  #236 commented on Jan 7, 2025 • 0 new comments

• E external/xla/xla/service/gpu/autotuning/gemm_fusion_autotuner.cc:1175] Results do not match the reference. This is likely a bug/unexpected loss of precision.

  #240 commented on Jan 9, 2025 • 0 new comments