Comments (7)
QiangZhang666ya
commented on September 14, 2024
hi, Dr. Gu, I would like to know how you get PDB files for protein sequences that are not included in alphafold2 database, download from the official website.
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ZhonghuiGu
commented on September 14, 2024
Hello! All sequences from the dataset I used are included in PDB database and AlphaFold2 database. If you want to predict sequences without predicted structures, you can utilize structure prediction tools like AlphaFold2, ESMFold, etc., to get a .pdb file for the input of HEAL.
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QiangZhang666ya
commented on September 14, 2024
Thank you for your answer. 1. Are you using the database swissprot_pdb_v4.tar? 2. The dataset format in articles is usually "11AS-A", but I did not find a PDB file named "11AS-A" in swissprot_pdb_v4.tar. May I ask how you are searching for PDB files?
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ZhonghuiGu
commented on September 14, 2024
You can download pdb file from Swiss-prot database through uniprot id.
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QiangZhang666ya
commented on September 14, 2024
Could you share my link for this data? uniprot id is "1s3p-a" or other?
…---- Replied Message ----
From ZhonghuiGu ***@***.***> Date 02/27/2024 22:46 To ZhonghuiGu/HEAL ***@***.***> Cc QiangZhang666ya ***@***.***>,
Author ***@***.***> Subject Re: [ZhonghuiGu/HEAL] how to get pdb files of proteins without in alphafold2 database (Issue #9)
You can download pdb file from Swiss-prot database through uniprot id.
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ZhonghuiGu
commented on September 14, 2024
"1s3p-a" may be a PDB id. I think you'd better first understand the origin of the dataset you use.
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QiangZhang666ya
commented on September 14, 2024
Thank you very much for your response to my inquiry. So, is it the process of looking up UniProt ID based on PDB ID, and then downloading the PDB file based on UniProt ID?
…---- Replied Message ----
From ZhonghuiGu ***@***.***> Date 02/27/2024 23:01 To ZhonghuiGu/HEAL ***@***.***> Cc QiangZhang666ya ***@***.***>,
Author ***@***.***> Subject Re: [ZhonghuiGu/HEAL] how to get pdb files of proteins without in alphafold2 database (Issue #9)
"1s3p-a" may be a PDB id. I think you'd better first understand the origin of the dataset you use.
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You are receiving this because you authored the thread.Message ID: ***@***.***>
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Related Issues (18)
- predictor.py error HOT 2
- Issues of unziping the dataset HOT 3
- Protein data with B chains could not be downloaded when collecting AF data HOT 2
- The download link for the dataset is no longer available. HOT 3
- HGT
- Unable to reproduce performance HOT 1
- Is the PDBch test set compared with DeepGO? Is the AFch test set compared with DeepGOPlus?
- dataset link not working
- About all model_*CLaf.pt
- Dataset link has expired
- model.load_state_dict(torch.load(f'model/model_{task}CL.pt',map_location=device)) error
- Urgent! Missing key(s) in state_dict of provided models HOT 3
- 段错误 (核心已转储) HOT 2
- graph input HOT 1
- Missing file: args.esm1b_model --contact- regression.pt HOT 3
- I would like to re-generate datasets such as train_graph.pt and train_pdbch.pt using a higher version of pyg HOT 5
- esm1b only supports input sequence lengths up to 1024, how to handle proteins with sequence lengths greater than 1024 HOT 1
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