openfold

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Enable Dropout in inference

1

Hello, I am trying to enable dropout during inference of the multimer model. This is enabled here for AlpaFold - https://github.com/bjornwallner/alphafoldv2.2.0/blob/9f76c2adf55403fd80b9079052716857d77a0396/alphafold/model/model.py#L80. Can you provide a pointer on how to enable...

tkramer-motion

- added mmseqs threads - added logging in run_pretrained_openfold.py - addition of scripts to generate feature pickle to json, coverage, pae and plddt plots in a colabfold alike display.

jflucier

How to emphasize on the structure?

1

Thank you for this great work. I learned a lot of insights of alphafold from openfold paper. I am predicting antibody-antigen complex. In my case, I already know the structure...

bzhousd

installation error

6

I tried to install openfold with the command: mamba env create -n openfold_env -f environment.yml and I get the following error: Downloading and Extracting Packages Preparing transaction: done Verifying transaction:...

abhinavb22

Hi, Does the Open Protein Set comes with Uniprot hits for the PDB proteins? I could find Uniref90, Mgnify, and BFD hits but not the UniProt hits, which are required...

abhinavb22

In data_transforms.py, the function make_msa_feat make protein's target_feat, and add has_beak is cat to target_feat, why? if i only want get the (N,21), can i get ride of first columns...

Paulie-ai

1.There is a missing space on line 32. 2.subdir is a relative path, not an absolute path. Therefore, according to the tutorial, it will not work. ChatGPT helped me fix...

smallfishabc

Unable to install OpenFold within Anaconda

1

I am currently trying to install OpenFold through the Anaconda command prompt, but I kept running into this issue when creating the environment: PackagesNotFoundError: The following packages are not available...

jimmyz100

Hi，I am using the recommended MMseqs2 alignment method from Colabfold pipeline. However, the script stucks for more than 24 hours for one chain (about 200 amino acids long). When I...

hanrthu

Unable to install OpenFold in Google Colaboratory

1

We are looking to utilize OpenFold within the implementation of NeuralPLexer and AlphaFlow, but when trying to pip install the package, this error keeps coming up: Building wheels for collected...

nickraisgit