def parse_mmcif(filename): """ 使用pdbx先构建仅蛋白的asym_id到entity_id的映射。 遍历所有asym_id,将每个asym_id 信息都装到chains中。 提取晶体结构的其他相关信息装到metadata中。 其实这里我做了修改,最早的脚本是使用pdb_strand_id作为中间桥梁,先将pdb_strand_id映射到asym_id,再映射到entity_id, ...
ClassNamea (UniProt)UniProt IDFunction (UniProt)Alternative functions Classical β-barrels 8-Stranded Empty Cell OmpA P0A910 Anchor between peptidoglycan and outer membrane Empty Cell OmpW P0A915 Uncharacterized Receptor for colicin S4 Empty Cell OmpX P0A917 Uncharacterized Empty Cell PagP [CrcA] ...
[17–19]. The number of proteins with the experimentally verified function is substantially lower than the number of newly discoveredprotein sequencesowing to the rapid advancement of genomics technology [20–22]. Among the 200 million sequences contained in the UniProt database, less than 1% ...
geneName/protein/:uniprotId/protein-features/. All APIs are easily accessible through the portal Swagger UI athttps://g2p.broadinstitute.org/api-docs/. The following databases are accessed by the portal: HUGO Genome Nomenclature Committee (https://www.genenames.org/), Ensembl browser (https:...
The dataset captures turnover rates that span >20-fold, and includes long-lived proteins such as histone H4 (Uniprot ID P62806; median half-life 54.6 days) and lamin-B1 (Uniprot ID P14733; median half-life 36.4 days), as well as fast turnover proteins such as apolipoprotein E (Uniprot...
It is the UniProt database. The UniProt database is known as a central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. Information such as the amino acid sequence, protein name, description of the protein, taxonomic data and citation ...
To identify the high-similarity proteins, blastpgp v2.2.26 (gapped-BLAST) was run with default parameters, using the training sequences as queries and the entire SP as target database (Altschul et al., 1997). #map the training sequences PDB IDs to UniProt IDs id_mapped='sets/id_mapped...
If you do not have a tool installed for folding protein structures, you can search for your protein by Uniprot ID in theAlphaFold database(https://alphafold.ebi.ac.uk/) without consuming resources for folding. Test on Your Own Dataset ...
with at least one atom within 6.5Å of any ligand atom. The database was carefully annotated by browsing severalprotein databases(PDB, UniProt, and GO) and storing, for every sc-PDB entry with the following features: protein name, function, source, domain and mutations, ligand name, and ...
Name: protein name in Uniprot knowledgebase. f Score: Mascot score. g # Peptides: number of identified peptides matching to the protein. h MW [kDa]: molecular weight of the protein expressed in kDa. These results revealed the identity of seven different deregulated proteins: Antithrombin-III ...