BMRBj Data Server:

common open representations of BMRB NMR-STAR data in XML, RDF, and JSON formats

BMRB/XML (complete):

Master (BMRB+Metabolomics)
https://bmrbpub.pdbj.org/archive/xml/
BMRB
https://bmrb.pdbj.org/ftp/pub/bmrb/entry_lists/xml/
Metabolomics
https://bmrb.pdbj.org/ftp/pub/bmrb/metabolomics/entry_lists/xml/

BMRB/XML (noatom):

Master (BMRB+Metabolomics)
https://bmrbpub.pdbj.org/archive/xml-noatom/
BMRB
https://bmrb.pdbj.org/ftp/pub/bmrb/entry_lists/xml-noatom/
Metabolomics
https://bmrb.pdbj.org/ftp/pub/bmrb/metabolomics/entry_lists/xml-noatom/

BMRB/RDF (RDF/XML):

Master (BMRB+Metabolomics)
https://bmrbpub.pdbj.org/archive/rdf/
BMRB
https://bmrb.pdbj.org/ftp/pub/bmrb/entry_lists/rdf/
Metabolomics
https://bmrb.pdbj.org/ftp/pub/bmrb/metabolomics/entry_lists/rdf/

BMRB/RDF (N-Triples):

Master (BMRB+Metabolomics)
https://bmrbpub.pdbj.org/archive/rdf-nt/
BMRB
https://bmrb.pdbj.org/ftp/pub/bmrb/entry_lists/rdf-nt/
Metabolomics
https://bmrb.pdbj.org/ftp/pub/bmrb/metabolomics/entry_lists/rdf-nt/

BMRB/JSON (noatom):

Master (BMRB+Metabolomics)
https://bmrbpub.pdbj.org/archive/json-noatom/
BMRB
https://bmrbpub.pdbj.org/archive/json-noatom/mmcif_nmr-star-v3.2.1.18 /bmr_json_noatom_doc/
Metabolomics
https://bmrbpub.pdbj.org/archive/json-noatom/mmcif_nmr-star-v3.2.1.18 /bms_json_noatom_doc/

Protein Blocks annotation (NMR structure):

https://bmrbpub.pdbj.org/archive/pb/

Protein Blocks annotation (Related X-ray structure):

https://bmrbpub.pdbj.org/archive/pb_xray/

FASTA sequence (BMRB):

https://bmrbpub.pdbj.org/archive/fasta/

FASTA sequence (PDB):

https://bmrbpub.pdbj.org/archive/fasta_pdb/

FASTA sequence (EMDB):

https://bmrbpub.pdbj.org/archive/fasta_emdb/

BLAST database (BMRB):

https://bmrbpub.pdbj.org/archive/blastdb/

BLAST database (PDB):

https://bmrbpub.pdbj.org/archive/blastdb_pdb/

BLAST database (EMDB):

https://bmrbpub.pdbj.org/archive/blastdb_emdb/

BLAST sequence alignement results (BMRB vs. BMRB, PDB, EMDB and UniProtKB):

https://bmrbpub.pdbj.org/archive/blastout/

BLAST sequence alignement results (PDB vs. BMRB, PDB, EMDB and UniProtKB):

https://bmrbpub.pdbj.org/archive/blastout_pdb/

BLAST sequence alignement results (EMDB vs. BMRB, PDB, EMDB and UniProtKB):

https://bmrbpub.pdbj.org/archive/blastout_emdb/

BLAST sequence alignement results (UniProtKB vs. BMRB, PDB, EMDB and UniProtKB):

https://bmrbpub.pdbj.org/archive/blastout_uniprotkb/

Combined NMR restraints (NMR-STAR or NEF):

https://bmrbpub.pdbj.org/archive/combined_restraints/
List of valid NMR restraints (NMR-STAR)
List of valid NMR restraints (NEF)
JSON Schema for NMR restraints report file

Chemical shift validation reports (JSON):

https://bmrbpub.pdbj.org/archive/cs_valid_reports/
JSON Schema for chemical shift validation report file

Completeness of assigned chemical shifts:

https://bmrbpub.pdbj.org/archive/cs_complete/
Excluded atoms from calculation of the completeness:
https://bmrbpub.pdbj.org/archive/cs_complete/excluded_atoms.str

MolProbity structure validation reports for all PDB entries (summary - oneline.csv):

https://bmrbpub.pdbj.org/archive/pdb_molprobity/oneline_files

MolProbity structure validation reports for all PDB entries (details - residue.csv):

https://bmrbpub.pdbj.org/archive/pdb_molprobity/residue_files

nmrML (FID) of BMRB metabolomics entries:

https://bmrbpub.pdbj.org/archive/bms-nmrml/

VRPT PDBML:

https://bmrbpub.pdbj.org/archive/pdbml-vrpt/
https://data.pdbj.org/pdbjplus/data/vrpt/xml-full/ (PDBj data server)

VRPT PDBML-alt:

https://data.pdbj.org/pdbjplus/data/vrpt/xml/ (PDBj data server)

VRPT/RDF:

https://bmrbpub.pdbj.org/archive/rdf-vrpt/
https://data.pdbj.org/pdbjplus/data/vrpt/rdf-full/ (PDBj data server)

VRPT/RDF-alt:

https://data.pdbj.org/pdbjplus/data/vrpt/rdf/ (PDBj data server)

VRPT mmCIF:

https://bmrbpub.pdbj.org/archive/mmcif-vrpt/
https://data.pdbj.org/pdbjplus/data/vrpt/mmcif-full/ (PDBj data server)

VRPT mmCIF-alt:

https://data.pdbj.org/pdbjplus/data/vrpt/mmcif/ (PDBj data server)

PDB/RDF:

https://data.pdbj.org/pdbjplus/data/pdb/rdf/ (PDBj data server)

chem_comp/RDF aka CCD:

https://data.pdbj.org/pdbjplus/data/cc/rdf/ (PDBj data server)

PRD/RDF aka BIRD:

https://data.pdbj.org/pdbjplus/data/prd/rdf/ (PDBj data server)

FAM/RDF aka BIRD:

https://data.pdbj.org/pdbjplus/data/family/rdf/ (PDBj data server)

BMRB/XML (complete):

% rsync -av --delete rsync://bmrbpub.pdbj.org/bmrb-xml .

BMRB/XML (noatom):

% rsync -av --delete rsync://bmrbpub.pdbj.org/bmrb-xml-noatom .

BMRB/RDF: (RDF/XML)

% rsync -av --delete rsync://bmrbpub.pdbj.org/bmrb-rdf .

BMRB/RDF (N-Triples):

% rsync -av --delete rsync://bmrbpub.pdbj.org/bmrb-rdf-nt .

BMRB/JSON (noatom):

% rsync -av --delete rsync://bmrbpub.pdbj.org/bmrb-json-noatom .

Protein Blocks annotation (NMR structure):

% rsync -avz --delete rsync://bmrbpub.pdbj.org/pb .

Protein Blocks annotation (Related X-ray structure):

% rsync -avz --delete rsync://bmrbpub.pdbj.org/pb-xray .

FASTA sequence (BMRB):

% rsync -avz --delete rsync://bmrbpub.pdbj.org/fasta .

FASTA sequence (PDB):

% rsync -avz --delete rsync://bmrbpub.pdbj.org/fasta-pdb .

FASTA sequence (EMDB):

% rsync -avz --delete rsync://bmrbpub.pdbj.org/fasta-emdb .

BLAST database (BMRB):

% rsync -av --delete rsync://bmrbpub.pdbj.org/blastdb .

BLAST database (PDB):

% rsync -av --delete rsync://bmrbpub.pdbj.org/blastdb-pdb .

BLAST database (EMDB):

% rsync -av --delete rsync://bmrbpub.pdbj.org/blastdb-emdb .

BLAST sequence alignement results (BMRB vs. BMRB, PDB, EMDB and UniProtKB):

% rsync -av --delete rsync://bmrbpub.pdbj.org/blastout .

BLAST sequence alignement results (PDB vs. BMRB, PDB, EMDB and UniProtKB):

% rsync -av --delete rsync://bmrbpub.pdbj.org/blastout-pdb .

BLAST sequence alignement results (EMDB vs. BMRB, PDB, EMDB and UniProtKB):

% rsync -av --delete rsync://bmrbpub.pdbj.org/blastout-emdb .

BLAST sequence alignement results (UniProtKB vs. BMRB, PDB, EMDB and UniProtKB):

% rsync -av --delete rsync://bmrbpub.pdbj.org/blastout-uniprotkb .

Combined NMR restraints (NMR-STAR or NEF):

% rsync -avz --delete rsync://bmrbpub.pdbj.org/mr .

Chemical shift validation reports (JSON):

% rsync -avz --delete rsync://bmrbpub.pdbj.org/cs-valid .

Completeness of assigned chemical shifts:

% rsync -avz --delete rsync://bmrbpub.pdbj.org/cs-complete .

MolProbity structure validation reports for all PDB entries (summary - oneline.csv):

% rsync -avz --delete rsync://bmrbpub.pdbj.org/molprobity-oneline .

MolProbity structure validation reports for all PDB entries (details - residue.csv):

% rsync -avz --delete rsync://bmrbpub.pdbj.org/molprobity-residue .

BMRB PostgreSQL dump file (noatom):

Initial setup:
% createdb -d $DB_NAME -U $DB_USER

Update:
% rsync -av --delete rsync://bmrbpub.pdbj.org/bmrb-pg-dump .
% pg_restore -c -d $DB_NAME -U $DB_USER bmrb_clone.sql

where $DB_NAME is database name and $DB_USER is user name.
PostgreSQL DDL:
https://bmrbpub.pdbj.org/schema/mmcif_nmr-star.dic.schema

nmrML (FID) of BMRB metabolomics entries:

% rsync -av --delete rsync://bmrbpub.pdbj.org/bms-nmrml .

PDBML-noatom PostgreSQL dump file:

Initial setup:
% createdb -d $DB_NAME -U $DB_USER

Update:
% rsync -av --delete rsync://bmrbpub.pdbj.org/pdbml-noatom-pg-dump .
% pg_restore -c -d $DB_NAME -U $DB_USER pdbml_noatom_clone.sql

where $DB_NAME is database name and $DB_USER is user name.
PostgreSQL DDL:
https://raw.githubusercontent.com/yokochi47/pdbx-validation/master/resource/pdbx-v50.sql

VRPT PDBML:

% rsync -av --delete rsync://bmrbpub.pdbj.org/pdbml-vrpt .

VRPT/RDF:

% rsync -av --delete rsync://bmrbpub.pdbj.org/rdf-vrpt .

VRPT mmCIF:

% rsync -av --delete rsync://bmrbpub.pdbj.org/mmcif-vrpt .

VRPT PDBML-alt PostgreSQL dump file:

Initial setup:
% createdb -d $DB_NAME -U $DB_USER

Update:
% rsync -av --delete rsync://bmrbpub.pdbj.org/pdbml-vrpt-alt-pg-dump .
% pg_restore -c -d $DB_NAME -U $DB_USER pdbml_vrpt_alt_clone.sql

where $DB_NAME is database name and $DB_USER is user name.
PostgreSQL DDL:
https://github.com/yokochi47/pdbx-validation/blob/master/schema/pdbx-validation-v4.sql

BioMagResBank:

Ulrich EL, Akutsu H, Doreleijers JF, Hrano Y, Ioannidis YE, Lin J, Linvy M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Wenger RK, Yao H, Markley JL, BioMagResBank, Nucleic Acids Research, 36, D402-D408 (2008)

BMRB/XML and BMRB/RDF:

Yokochi M, Kobayashi N, Ulrich EL, Kinjo AR, Iwata T, Ioannidis YE, Linvy M, Markley JL, Nakamura H, Kojima C, Fujiwara T, Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins, J. Biomed. Semantics, 7(1), 16 (2016)

BMRB/JSON:

Kinjo AR, Bekker GJ, Wako H, Endo S, Tsuchiya Y, Sato H, Nishi H, Kinoshita K, Suzuki H, Kawabata T, Yokochi M, Iwata T, Kobayashi N, Fujiwara T, Kurisu G, Nakamura H, New tools and functions in data-out activities at Protein Data Bank Japan (PDBj), Protein Science, 27(1), 95-102 (2018)

nmrML:

Schober D, Jacob D, Wilson M, Cruz JA, Marcu A, Grant JR, Moing A, Deborde C, de Figueiredo LF, Haug K, Rocca-Serra P, Easton JM, Ebbels TMD, Hao J, Ludwig C, Günther UL, Rosato A, Klein MS, Lewis I, Luchinat C, Jones AR, Grauslys A, Larralde M, Yokochi M, Kobayashi N, Porzel A, Griffin J, Viant MR, Wishart DS, Steinbeck C, Salek RM, Neumann S., nmrML: a community supported open data standard for the description, storage, and exchange of NMR data, Analytical Chemistry, 90(1), 649-656 (2017)

NMR-STAR:

Ulrich EL, Baskaran K, Dashti H, Ioannidis YE, Livny M, Romero PR, Maziuk D, Wedell JR, Yao H, Eghbalnia HR, Hoch JC, Markley JL, NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments, J. biomol. NMR, ePub ahead, 1-5 (2018)

Protein Blocks:

Joseph AP, Agarwal G, Mahajan S, Gelly JC, Swapna LS, Offmann B, Cadet F, Bornot A, Tyagi M, Valadié H, Schneider B, Etchebest C, Srinivasan N, De Brevern AG, A short survey on protein blocks, Biophys Rev. 2010 Aug;2(3):137-147. Epub 2010 Aug 5.

Tyagi M, Sharma P, Swamy CS, Cadet F, Srinivasan N, de Brevern AG, Offmann B, Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet, Nucleic Acids Res. 2006 Jul 1;34 (Web Server issue):W119-23

MolProbity:

Vincent B. Chen, W. Bryan Arendall III, Jeffrey J. Headd, Daniel A. Keedy, Robert M. Immormino, Gary J. Kapral, Laura W. Murray, Jane S. Richardson and David C. Richardson (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66: 12-21

Ian W. Davis, Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, Laura W. Murray, W. Bryan Arendall III, Jack Snoeyink, Jane S. Richardson and David C. Richardson (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research 35: Web Server issue, W375-W383

NEF (NMR Exchange Format):

Gutmanas, A., Adams, P., Bardiaux, B. et al. NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol 22, 433–434 (2015). https://doi.org/10.1038/nsmb.3041