MAPE-PPI

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About the Training Process

6

Dear Authors, Do you release the training code? How long does this method need to train?

AmingWu

About CATH dataset pretraining

2

Dear author, you have a pre-trained model on github, on which dataset was this model pre-trained? In your paper, you mentioned using the CATH dataset for pre-training. I think it...

yuanhu246

File not found

1

Helllo Author, ./raw_data/data_process.py file not found. How can I get this file? Thank you~

zzw1402623669

The node representation from ESM1b

1

I am interested in Mape-PPI and its relevant baseline methods. I would like to ask whether global representations (embeddings from the CLS token) or averaged/pooled residue-level representations should be used...

UR-Free

Clarification on the all_assign.txt File Format and Column Definitions

2

I am currently using the all_assign.txt file in the MAPE-PPI repository and I am trying to understand its format and purpose more clearly. Could you please provide some details about...

jjjjjqt

Dear authors, I have followed you description in the README to download the CATH42 datasets and processed it into protein.rball.edges.CATH42.npy, protein.knn.edges.CATH42.npy, protein.nodes.CATH42.pt. I directly use your codes and the following...

yzf-code

Guidance required on how to upload amino acid sequence/PDB files of two proteins to check interactions between them.

1

It is not clear anywhere how to upload my data (amino acid sequence or PDB file?) for running a job to check interactions between two proteins I want to upload...

u7068758

environment.yml fails

3

I was using your environment.yml and it fails: ResolvePackageNotFound: - nni==2.10 - json==2.0.9 - dgl==0.9.1post1 - csv==1.0 - argparse==1.1 Firstly, is not argparse, json, csv standard python libraries not conda...

fishpm-anu

protein sequences do not match the sequences in the pdb file

1

I found that in the protein.SHS27k.sequences.dictionary.tsv file, some of the protein sequences do not match the sequences in the pdb file. Could you please clarify which one should be taken...

Joe-Alwyn