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flatironinstitute/deepblast
tm_vec_cath_model.ckpt and tm_vec_cath_model_params.json unavailable

Hi, Thank you for engineering this cool tool! I came across the following error. Specifically, when downloading the ckpt and json files, I get a 403 error $ wget https://users.flatironinstitute.org/thamamsy/public_www/tm_vec_cath_model.ckpt ...
  • JLSteenwyk
  • 2
  • Opened 
    on Feb 23
  • #170

flatironinstitute/deepblast
Test dataset for CATHS40

Hi, the CATHS40 training database is provided in the article, and I would like to know if it is possible to provide the protein of the test set and validation set of the CATHS40 mentioned in the paper ...
  • haniulu
  • Opened 
    on Jan 15
  • #169

flatironinstitute/deepblast
Comparison between two sequences

Can it specify two sequences for comparison and get the predicted value of TMScore of the corresponding structures of these two sequences?Thanks
  • AIM132
  • 5
  • Opened 
    on Dec 23, 2024
  • #167

flatironinstitute/deepblast
Missing validation metrics

We should add the validation metrics back in the next release. See here where the commented validation metrics are removed. https://github.com/flatironinstitute/deepblast/pull/165
  • mortonjt
  • Opened 
    on Nov 11, 2024
  • #166

flatironinstitute/deepblast
link for downloading deepblast checkpoints in wiki returns a 404

image In the Aligning Proteins wiki article, it is recommended to download the model checkpoints from the following link: https://users.flatironinstitute.org/jmorton/public_www/deepblast-public-data/checkpoints/deepblast-v3.ckpt ...
  • aryankeluskar
  • 1
  • Opened 
    on Nov 4, 2024
  • #164

flatironinstitute/deepblast
Error While Downloading DeepBLAST Model and Database

While trying to install the DeepBLAST model and the associated database using the provided wget commands, I encountered an error indicating that the model file could not be found. Below are the steps I ...
  • khatrics16
  • 1
  • Opened 
    on Jul 25, 2024
  • #162

flatironinstitute/deepblast
Model download link failed

Dear the author: Hello! I want to test vm-vec and deepblast. However, this link https://users.flatironinstitute.org/thamamsy/public_www/tm_vec_swiss_model.ckpt returns a 404 error. Additionally, the link ...
  • yuanwenguang666
  • 2
  • Opened 
    on Jul 3, 2024
  • #161

flatironinstitute/deepblast
Pretraind model download

Hi, I m trying to download the weights of the pre-built model as described in the Searching proteins guide. Unfortunately, wget fails as follows: wget https://users.flatironinstitute.org/thamamsy/public_www/tm_vec_cath_model.ckpt ...
  • gbrsales
  • 7
  • Opened 
    on May 13, 2024
  • #160

flatironinstitute/deepblast
Feasible approach to build a large database

Hello, I am trying to build a database from the NCBI nr FASTA (707338897 entries) for more extensive protein search. I have tried to split up the FASTA into smaller chunks (about 250 entries per run) and ...
  • yzlwk
  • 1
  • Opened 
    on Apr 22, 2024
  • #159

flatironinstitute/deepblast
TM-score calculation for DeepBlast

Hi, Thank you so much for this excellent work! I am a newer in protein alignment and may test this method in my project. I only have protein sequence data and I would like to check their similarity using ...
  • zh-qifan
  • 4
  • Opened 
    on Mar 26, 2024
  • #156
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