PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.

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 o...

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Autores principales:	Bulat Faezov, Roland L Dunbrack
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7f3f0cfc76ae4757a2a52e26dc666046
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spelling	oai:doaj.org-article:7f3f0cfc76ae4757a2a52e26dc6660462021-12-02T20:05:12ZPDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.1932-620310.1371/journal.pone.0253411https://doaj.org/article/7f3f0cfc76ae4757a2a52e26dc6660462021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0253411https://doaj.org/toc/1932-6203The 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.Bulat FaezovRoland L DunbrackPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 7, p e0253411 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bulat Faezov Roland L Dunbrack PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.
description	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.
format	article
author	Bulat Faezov Roland L Dunbrack
author_facet	Bulat Faezov Roland L Dunbrack
author_sort	Bulat Faezov
title	PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.
title_short	PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.
title_full	PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.
title_fullStr	PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.
title_full_unstemmed	PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.
title_sort	pdbrenum: a webserver and program providing protein data bank files renumbered according to their uniprot sequences.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/7f3f0cfc76ae4757a2a52e26dc666046
work_keys_str_mv	AT bulatfaezov pdbrenumawebserverandprogramprovidingproteindatabankfilesrenumberedaccordingtotheiruniprotsequences AT rolandldunbrack pdbrenumawebserverandprogramprovidingproteindatabankfilesrenumberedaccordingtotheiruniprotsequences
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PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences.

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