Igor Tolstoy

>5NGM_Ab 30S ribosomal protein S2; Ribosome Cryo-EM Structural Biology Hibernation; HET: MG; 2.9A {Staphylococcus aureus} MAVISMKQLLEAGVHFGHQTRRWNPKMKKYIFTERNGIYIIDLQKTVKKVDEAYNFLKQVSEDGGQVLFVGTKKQAQESV KSEAERAGQFYINQRWLGGLLTNYKTISKRIKRISEIEKMEEDGLFEVLPKKEVVELKKEYDRLIKFLGGIRDMKSMPQA LFVVDPRKERNAIAEARKLNIPIVGIVDTNCDPDEIDYVIPANDDAIRAVKLLTAKMADAILEGQQGVSNEEVAAEQNID LDEKEKSEETEATEE >5NGM_Ac 30S ribosomal protein S3; Ribosome Cryo-EM Structural Biology Hibernation; HET:...

https://ftp.ncbi.nlm.nih.gov/genomes/Viruses/FamilyPhylogeneticTree/Graph/cif2fasta.py possible fix for 5NGM. but need to be checked on whole pdb.

I can , but it is not “complete” fix It is very serious change in code which change names for whole pdb. I just don’t know exactly how pull request...

problem with pdbx_descriptor is very serious my current cif2fasta crash on 4v61, it could be fixed , but pdbx_descriptor contain just one word "Ribosome" real proteins names you can find...

probably,you will be interested I have created map (july 21,2022) from sequence crc64 (GCP bigquery deepmind AF metainfomation table) to alphafold/uniprot and genbank accessions. map contain ~2G rows because uniprot/genbank/alphafold...

http://www0.cs.ucl.ac.uk/staff/d.jones/crcnote.pdf known problem with alphafold/uniprot crc64 : I have found ~500 sequences pairs in AF universe with the same crc64, but different only in two positions with step 8: looks...

continue.. I have found EsmAtlas and Alphafold 3D-structures with identical protein sequences and average pLDDT > 90% on both ends and then compare 3Di sequences, global 100-pident distribution you can...

feature assignments looks a little bit unstable for 0.99 tm-score i - j fluctuations: 6 1 -4 10 -1 -3 24 -1 4 36 -1 -3 52 -4 4 58...

https://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/ just clarification: I am interested download your uniref90 database with embeddings, not uniref90 fastas itself.

Do you have access to AWS S3? s3://serratus-public/igortu/metabuli.VMR.39/ or https://serratus-public.s3.amazonaws.com/igortu/metabuli.VMR.39/ This directory contains all required files including dmp and nucleotide fasta >2Gb. whole VMR taxonomy now has new taxids incompatible...