sokrypton / ColabDesign

Making Protein Design accessible to all via Google Colab!

sokrypton/ColabDesign Issues

Can af_cyc_design generate cyclic pepitide with D-Amino acid
Updated 4 months ago1
binders designed don't binds at the hotspots of the target chain.
Updated 4 months ago
Is it preferable for the "con" metric to have a smaller value during the optimization process?
Updated 6 months ago
af_model.predict failing
Closed 6 months ago2
How to predict the Cyclic Peptide's structure by a given sequence
Updated 7 months ago3
mk_af_model: refolding a sequence of a experimental structure using said structure as a template performs miserably
Closed 7 months ago2
converting other MPNN checkpoints for support in ColabDesign and JAX
Updated 8 months ago8
why colabdesign alphafold limits on insertion code at chain
Closed 8 months ago
XlaRuntimeError: FAILED_PRECONDITION: DNN library initialization failed.
Closed 8 months ago1
How to design more binders
Closed a year ago2
Locally Run ColabDesign
Updated 10 months ago
Is the "i_pae" score in the designability_test.py the same as pAE_interaction?
Updated a year ago
Contigs messed up with partial diffusion and manual symmetry
Updated a year ago
How to continue a design run?
Updated a year ago
Partially folding a structure using AF
Updated a year ago
fix_pos in af/fixbb
Updated a year ago2
Do the soft iterations in pssm_semigreedy obey the bias matrix
Updated a year ago
where is the output file when finish the model.design_3stage() run?
Updated a year ago1
Is it possible to bypass the design step of AfDesign?
Updated a year ago
Can we see generated sequences other than final one?
Updated a year ago1
How to get PAE files when running RFdiffusion
Updated a year ago
Allow to select the Complex_beta_ckpt model in RFdiffusion colab?
Updated a year ago
Translate colab for RFdiffusion to a jupyter notebook?
Updated a year ago
Patch fix_partial_contigs when residue numbering in PDB has a gap
Updated a year ago2
MPNN designed sequence not separated correctly with multiple targets and multiple binders
Updated a year ago2
Any plans to add af2seq to the colab design
Updated a year ago
The sequence in design.fasta is different from the sequence in best.pdb
Closed a year ago5
atom index in af.prep.prep_pdb
Updated a year ago1
Using RFdiffusion to design a binder, with some parts of the binder fixed
Updated a year ago6
WARNING: 'model_1_ptm' not found
Closed a year ago1
Problem in designability_test.py
Closed a year ago2
how to interpret results of 'use_templates=True' versus 'False' in partial_hallucination_rewire?
Updated a year ago1
critical typo in kmeans.py (simport instead of import)
Updated a year ago1
Minimize sequence length while preserving some amount of structural stability.
Updated a year ago
OOM on AF DB proteins?
Updated a year ago2
small fix required for newer numpy versions
Updated a year ago
pLDDT increases and then decreases during the soft iterations
Updated a year ago8
git clone error
Updated 2 years ago2
Fix sequence at certain positions in Binder protocol
Updated 2 years ago8
How to use gpu or cuda for design binder
Updated 2 years ago1
Out of memory error
Updated 2 years ago4
out of memory for partial hallucination
Updated 2 years ago2
'mk_af_model' object has no attribute 'aux'
Closed 2 years ago6
difference between plddt in the log and in the saved PDB!
Closed 2 years ago2
Homooligomer design in ProteinMPNN
Closed 2 years ago2
Sidechain rmsd loss throws out error
Closed 2 years ago2
Add seed
Closed 2 years ago2
partial hallucination with multiple chains
Updated 2 years ago2
TypeError: tree_map() missing 1 required positional argument: 'tree'
Closed 2 years ago16
Binder Hallucination Memory Leak
Closed 2 years ago4