Antonio Fonseca

Hi, I am trying to use DeepExplain with the [Concept Saliency Map](https://github.com/lenbrocki/concept-saliency-maps). However, I run into the following issue: ``` import keras sess = K.get_session() print('sess: ',sess) from ConceptSaliencyMaps.deepexplain.tensorflow import...

Problems during backward

6

Hi, Firts of all, thank you for sharing your code. I would like to use your interpolation during training, but unfortunately, I get the following error message during the backward...

Connection refused - fingerprint

1

Hi! Thank you for the useful tutorial. It was very good. I am facing an issue: Error: SSL error 40 HTTP GET failed with code -1 I already have my...

Hi, I would like to compute the TM-score between my newly generated protein and the entire PDB dataset, similarly to what you show in Figure 2b. Could you please point...

Having issues to create a NR db with taxonomy info

7

I would like to run the seq similarity search against the homo sapien samples in the NR dataset. For that I downloaded the dataset as follows: `mmseqs databases NR nr...

convertails getting killed due to the memory

1

mmseqs gets killed when saving the output: ``` convertalis /tmp/queryDB /root/mmseqs2_db/swissprot_human /tmp/resultDB resultDB.tab --format-output query,target,evalue,qaln,taln,taxname,pident,cigar MMseqs Version: 15.6f452 Substitution matrix aa:blosum62.out,nucl:nucleotide.out Alignment format 0 Format alignment output query,target,evalue,qaln,taln,taxname,pident,cigar Translation table...

Difference in evalue when doijng search against swissprot_human and swissprot

2

I would like to find the closest human protein sequence for any given query. Often the query sequences are short (10aa). To test if mmseq could help with that, I...

Hi, I am trying to follow the steps to download the db to run the MSA locally. I have used the download script to get uniref30. The download seems to...

Hi, I have two proteins that I would like to test the docking. I have adapted your example script (single_pairs) to run with my proteins. The output of the DiffDock...

Hi, I am getting the following error when running the inference example using the two provided pdb files: ``` Traceback (most recent call last): File "/root/DiffDock-PP/src/main_inf.py", line 620, in main()...