FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3181892255> ?p ?o ?g. }

• W3181892255 endingPage "e0253411" @default.
• W3181892255 startingPage "e0253411" @default.
• W3181892255 abstract "The Protein Data Bank (PDB) was established at Brookhaven National Laboratories in 1971 as an archive for biological macromolecular crystal structures. In mid 2021, the database has almost 180,000 structures solved by X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and other methods. Many proteins have been studied under different conditions, including binding partners such as ligands, nucleic acids, or other proteins; mutations, and post-translational modifications, thus enabling extensive comparative structure-function studies. However, these studies are made more difficult because authors are allowed by the PDB to number the amino acids in each protein sequence in any manner they wish. This results in the same protein being numbered differently in the available PDB entries. For instance, some authors may include N-terminal signal peptides or the N-terminal methionine in the sequence numbering and others may not. In addition to the coordinates, there are many fields that contain structural and functional information regarding specific residues numbered according to the author. Here we provide a webserver and Python3 application that fixes the PDB sequence numbering problem by replacing the author numbering with numbering derived from the corresponding UniProt sequences. We obtain this correspondence from the SIFTS database from PDBe. The server and program can take a list of PDB entries or a list of UniProt identifiers (e.g., P04637 or P53_HUMAN) and provide renumbered files in mmCIF format and the legacy PDB format for both asymmetric unit files and biological assembly files provided by PDBe." @default.
• W3181892255 created "2021-07-19" @default.
• W3181892255 creator A5053977807 @default.
• W3181892255 creator A5057395358 @default.
• W3181892255 date "2021-07-06" @default.
• W3181892255 modified "2023-10-14" @default.
• W3181892255 title "PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences" @default.
• W3181892255 cites W1551915691 @default.
• W3181892255 cites W1997311863 @default.
• W3181892255 cites W2022265858 @default.
• W3181892255 cites W2035503835 @default.
• W3181892255 cites W2108877315 @default.
• W3181892255 cites W2109872885 @default.
• W3181892255 cites W2162388472 @default.
• W3181892255 cites W2163508726 @default.
• W3181892255 cites W2168172687 @default.
• W3181892255 cites W2342249984 @default.
• W3181892255 cites W2747261161 @default.
• W3181892255 cites W2898364362 @default.
• W3181892255 cites W2900674118 @default.
• W3181892255 cites W3136918052 @default.
• W3181892255 cites W4236459334 @default.
• W3181892255 cites W2164892500 @default.
• W3181892255 doi "https://doi.org/10.1371/journal.pone.0253411" @default.
• W3181892255 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8259974" @default.
• W3181892255 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/34228733" @default.
• W3181892255 hasPublicationYear "2021" @default.
• W3181892255 type Work @default.
• W3181892255 sameAs 3181892255 @default.
• W3181892255 citedByCount "12" @default.
• W3181892255 countsByYear W31818922552021 @default.
• W3181892255 countsByYear W31818922552022 @default.
• W3181892255 countsByYear W31818922552023 @default.
• W3181892255 crossrefType "journal-article" @default.
• W3181892255 hasAuthorship W3181892255A5053977807 @default.
• W3181892255 hasAuthorship W3181892255A5057395358 @default.
• W3181892255 hasBestOaLocation W31818922551 @default.
• W3181892255 hasConcept C10010492 @default.
• W3181892255 hasConcept C104317684 @default.
• W3181892255 hasConcept C119145174 @default.
• W3181892255 hasConcept C136475424 @default.
• W3181892255 hasConcept C141231307 @default.
• W3181892255 hasConcept C141674004 @default.
• W3181892255 hasConcept C151810110 @default.
• W3181892255 hasConcept C154504017 @default.
• W3181892255 hasConcept C167625842 @default.
• W3181892255 hasConcept C189206191 @default.
• W3181892255 hasConcept C191916993 @default.
• W3181892255 hasConcept C199360897 @default.
• W3181892255 hasConcept C202264299 @default.
• W3181892255 hasConcept C2778112365 @default.
• W3181892255 hasConcept C41008148 @default.
• W3181892255 hasConcept C41584329 @default.
• W3181892255 hasConcept C45484198 @default.
• W3181892255 hasConcept C47701112 @default.
• W3181892255 hasConcept C54355233 @default.
• W3181892255 hasConcept C55493867 @default.
• W3181892255 hasConcept C60644358 @default.
• W3181892255 hasConcept C65556437 @default.
• W3181892255 hasConcept C70721500 @default.
• W3181892255 hasConcept C77088390 @default.
• W3181892255 hasConcept C86803240 @default.
• W3181892255 hasConceptScore W3181892255C10010492 @default.
• W3181892255 hasConceptScore W3181892255C104317684 @default.
• W3181892255 hasConceptScore W3181892255C119145174 @default.
• W3181892255 hasConceptScore W3181892255C136475424 @default.
• W3181892255 hasConceptScore W3181892255C141231307 @default.
• W3181892255 hasConceptScore W3181892255C141674004 @default.
• W3181892255 hasConceptScore W3181892255C151810110 @default.
• W3181892255 hasConceptScore W3181892255C154504017 @default.
• W3181892255 hasConceptScore W3181892255C167625842 @default.
• W3181892255 hasConceptScore W3181892255C189206191 @default.
• W3181892255 hasConceptScore W3181892255C191916993 @default.
• W3181892255 hasConceptScore W3181892255C199360897 @default.
• W3181892255 hasConceptScore W3181892255C202264299 @default.
• W3181892255 hasConceptScore W3181892255C2778112365 @default.
• W3181892255 hasConceptScore W3181892255C41008148 @default.
• W3181892255 hasConceptScore W3181892255C41584329 @default.
• W3181892255 hasConceptScore W3181892255C45484198 @default.
• W3181892255 hasConceptScore W3181892255C47701112 @default.
• W3181892255 hasConceptScore W3181892255C54355233 @default.
• W3181892255 hasConceptScore W3181892255C55493867 @default.
• W3181892255 hasConceptScore W3181892255C60644358 @default.
• W3181892255 hasConceptScore W3181892255C65556437 @default.
• W3181892255 hasConceptScore W3181892255C70721500 @default.
• W3181892255 hasConceptScore W3181892255C77088390 @default.
• W3181892255 hasConceptScore W3181892255C86803240 @default.
• W3181892255 hasFunder F4320337354 @default.
• W3181892255 hasIssue "7" @default.
• W3181892255 hasLocation W31818922551 @default.
• W3181892255 hasLocation W31818922552 @default.
• W3181892255 hasLocation W31818922553 @default.
• W3181892255 hasLocation W31818922554 @default.
• W3181892255 hasLocation W31818922555 @default.
• W3181892255 hasOpenAccess W3181892255 @default.
• W3181892255 hasPrimaryLocation W31818922551 @default.
• W3181892255 hasRelatedWork W1972394537 @default.
• W3181892255 hasRelatedWork W1984316389 @default.

• next