Igor Tolstoy
Igor Tolstoy
cif2fasta.py (3.2.0) incorrectly generate protein description when cif file contain multiple fasta
code : protein_description = struct.getValue('pdbx_descriptor') protein_description = protein_description.replace('\n', ' ') protein_description = protein_description.replace(';', ' ') # to prevent parsing errors if len(protein_description.split(' ')) >= 5: protein_description = ' '.join(protein_description.split(' ')[0:5])...
1) https://search.foldseek.com/queue/Z2fX2gw_ZuE4fLFe1iI-MSF4W-Sj2jktXz1nvw I have searched https://tinyurl.com/39hdture or https://tinyurl.com/bdz38eeh 2) foldseek structureto3didescriptor AF-A0A009GDF2-F1-model_v4.cif.1.cif AF-A0A009GDF2-F1-model_v4.cif.1.cif.3di produce empty output. files looks ok when I load them using: https://www.rcsb.org/3d-view if I export cif files...
“We also offer the option to use TM-align for pairwise structure alignment instead of the 3Di-based alignment. We implemented TM-align based on the Cα atom coordinates and made adjustments to...
Hello, I want to try reproduce your results for ./learnAlphabet.sh 20 100 data/pdbs_train.txt data/pdbs_val.txt out/ is it possible provide some intermediate data for comparison? log.txt, final round fasta, alignments scores,etc....
I would suggest you rebuild kraken2 viral reference database using current official viral taxonomy provided on https://ictv.global/vmr. according your publication kraken2 viruses database based on viral refseq which is technically...
I would suggest rebuild metabuli viral reference database using current official viral taxonomy provided on https://ictv.global/vmr Technically, it is not difficult. Your tool processed it very smoothly. If interested, I...