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I think it might be time to dip our toe back into the Google Summer of Code project, this time through the [Open Bioinformatics Foundation](https://summerofcode.withgoogle.com/organizations/5447537956…
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I'm trying to generate a model using a map generated in cryosparc and protein fasta file. The process runs through the Initial C-alpha prediction phase and then terminates, leaving behind an empty out…
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Dear Khalak,
I found there are many clashes when aligning the decoupled structures of ligands in solvent into the apo state pocket. And some of them cannot be solved by just do a minimization and t…
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I would like to know what is the exact dataset used to generate the toy_ppi dataset in example_data folder (input files used to generate the pre-processed dataset). What are the node features availabl…
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Copy of thread from the list:
Hi Matt,
(hide our dirty laundry) "As much as possible? Just get rid of the spectra, the
XML, and the ambiguity groups! :) MzIdentML is clearly not intended for
e…
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**Is your feature request related to a problem? Please describe.**
Currently, we only support PDB files as inputs for protein structure graphs. [Large complexes are now unavailable as PDBs.](https://…
a-r-j updated
2 years ago
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How can we use protein sequence as receptor input and ligand smiles file as a ligand input?
I tried to use fasta format or txt format for the sequence of my protein but I got an error as " can only j…
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## Context:
I want to search for structure matches ONLY for "representative" proteins in the proteome of my species of interest, and I would rather build the searchable database using just these IDs,…
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### Question
I want to add a graph to the observation space by
```
# Create NetworkX graph
G = nx.Graph()
# Add nodes (C-alpha atoms) with 320-dimensional zero embeddings
for _, ro…
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Please make sure other downloads are done properly