nrbennet/dl_binder_design

Issues

• <class 'IndexError'> when using dl_interface_design.py

  #56 opened 10 months ago by aw10279
  4

• Parallelization?

  #93 opened a month ago by Epannec
  0

• In lab experiment, binding affinity is pretty strong, but pae_interaction is only around 28

  #82 opened 5 months ago by Huilin-Li
  2

• SCOPData Deprecated in Latest Biopython

  #92 opened 2 months ago by mnoyes68
  0

• after af2_initial_guess/predict.py, the distance between binder and target becomes much longer

  #79 opened 2 months ago by rocke2020
  0

• weird random error No such file or directory: 'temp.pdb' and -temperature: command not found

  #89 opened 2 months ago by 18217265596
  0

• FileNotFoundError in dl_binder_design when running multiple silent files in parallel

  #88 opened 2 months ago by xuqiqin
  0

• Issue with predict.py utput

  #87 opened 2 months ago by Bilal0101-debug
  0

• in af2_initial_guess/predict.py PDB mode skips checkpoints due to inconsistent naming in self.finished_structs

  #86 opened 2 months ago by xuqiqin
  0

• Question about AF2 model weights

  #73 opened 7 months ago by Artolomeus
  1

• dl_binder_design af2_initial_guess not functioning

  #85 opened 2 months ago by A2t3m15
  0

• An error occurred during the testing of the ProteinMPNN FastRelax Environment.

  #83 opened 5 months ago by AIM132
  2

• Unable to connect to GPU

  #80 opened 5 months ago by david1234janitor
  1

• dl_interface_design.py does not like scaffolds with periods

  #84 opened 5 months ago by drewschaub
  0

• error with af2_binder_design.yml - ImportError: cannot import name 'SCOPData' from 'Bio.Data - wrong version of biopython

  #72 opened 7 months ago by drewschaub
  1

• Segementation fault: pyrosetta & tensorflow

  #50 opened a year ago by charbj
  3

• Some confusion about the results

  #81 opened 5 months ago
  0

• Any chance to share a docker or apptainer file?

  #78 opened 6 months ago by yilunqi
  0

• make_msa_features "unexcpected input=deletion_matrices"

  #77 opened 6 months ago by rmdelaney13
  0

• insert_Rosetta_chainbreaks has an incorrect method signature

  #76 opened 6 months ago by jonlevi
  0

• Floating point exception (Segmentation fault) when testing the conda env from af2_binder_design.yml

  #68 opened 8 months ago by daniel-sali
  3

• segmentation fault (core dumped) when running predict.py in af2_binder_design

  #69 opened 8 months ago by MadelineMartin
  4

• Complex error - cuDNN/CuFFT/Numpy version(?)

  #75 opened 6 months ago by Avidhoot26
  1

• For reproducing RFdiffusion experiment

  #74 opened 7 months ago by haoyuanli66
  0

• af2_complex_rmsd score?

  #58 opened 10 months ago by caleblareau
  3

• More than two chains?

  #30 opened a year ago by okanders
  2

• How to use the addFIXEDlabels.py script, what is the meaning for trb

  #70 opened 8 months ago by ning-2022
  0

• Structure with tag designed_tag failed in 0 seconds with error: <class 'IndexError'>

  #37 opened a year ago by Deoyeh
  1

• Sampling Temperature

  #66 opened 8 months ago by johnny-rodriguez
  0

• Majority of the sequence is composed of lysines

  #65 opened 9 months ago by ackbar03
  0

• Segmentation fault (core dumped) for CUDA12

  #60 opened 9 months ago by danboshuiyan
  7

• Is "AF2 initial guess" supposed to have access to the standard AF2 databases?

  #57 opened 10 months ago by rszabla
  3

• differenct result of the AF2 initial guess for the same protein

  #53 opened 10 months ago by jongseo-park
  6

• af2_complex_error

  #41 opened 10 months ago by pedrovaliente79
  2

• Any reason why cysteine is ommitted by default in ProteinMPNN? Or is that just an accident?

  #55 opened 10 months ago by ackbar03
  1

• Minimized AF2 predictions

  #51 opened 10 months ago by almeida85
  2

• ml_dtypes > 0.2 breaks the af2_binder_design environment

  #52 opened a year ago by rszabla
  1

• af2_complex running error

  #40 opened a year ago by pedrovaliente79
  1

• Run dl_binder_design with already generated backbones

  #47 opened a year ago by plvdac1
  1

• Guidance Needed: Specifying GPU for AF2_initial_guess

  #49 opened a year ago by assiduous006
  4

• Jupyter notebook available?

  #29 opened a year ago by slives-lab
  1

• RuntimeError: jaxlib/cusolver.cc:51: operation cusolverDnCreate(&handle) failed: cuSolver internal error

  #38 opened a year ago by SupermeCJ
  1

• tensorflow 2.12.1 requires jax>=0.3.15

  #31 opened a year ago by frankligy
  2

• for symmetric multimers

  #36 opened a year ago by jongseo-park
  1

• GPU error: Segmentation fault (core dumped)

  #33 opened a year ago by ning-2022
  2

• Conda environment setup does not work

  #39 opened a year ago by brystingjosephine
  1

• runlist no output

  #42 opened a year ago by jelka71
  1

• Is it possible to inpaint a missing part of a protein and designing sequences using the dl_binder_design?

  #43 opened a year ago by wangdoc2002
  1

• example script for <<inputs/pdbs /design_ppi_0.pdb>>

  #46 opened a year ago by 21tesla
  1

• Deep Learning Binder Results

  #32 opened a year ago by okanders
  2