Ruben Alvarez

mapping inconsistency between using reference sequence in command line or fastq file

2

Hello, I am getting a unique mapping with bowtie2 providing a reference sequence inline or in fasta, vs one mapping plus a secondary mapping when providing a fastq file. Why...

PeSTo/md_analysis/data_manager /data_manager.py, "meta" does not exist

2

I have tried to run PeSTo/md_analysis/apply_model_md.ipynb. The folder "model" does not exist here, but I copied it from the root directory. The from X import statements need to refer to...

interface_ppi_confidence.ipynb, missing data and incorrect module calling

6

Modules are not called according to the repository structure, eg: `from model import Model` should be `from model.model import Model` Also, example data missing: `dataset = Dataset("datasets/contacts_rr5A_64nn_8192.h5")` I could suggest...

The results file below is missing from the repository, so the .ipynb notebook cannot be run: results/interface_ppi_cuda_profiling.csv

question - are all protein pairs direct interactors?

2

I was thinking of using DIPS-Plus for training a classifier for protein-protein interaction (I confess I have little experience in ML, any advice welcome). The database describes the pairs based...

Not issue, but question: can it do reverse screening?

1

Such a great contribution. It occurred to me, can boltz do reverse screening, i.e. for a drug screen a library of targets (drug repurposing goal)?

Hello, Not sure if this is a bug or expected behaviour, but the png matches the rendered aligned image:  whilst the pdb does not (it looks like either the...

Hello, since the last update from uniclust is 2017, is hhblits less relevant now? Can it be used with uniref clusters? Or is there a different hhblits-like engine to use...