PDBj-BMRB Data Server:

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

BMRB/XML (complete):

Master (BMRB+Metabolomics)
http://bmrbpub.protein.osaka-u.ac.jp/archive/xml/
BMRB
http://bmrb.pdbj.org/ftp/pub/bmrb/entry_lists/xml/
Metabolomics
http://bmrb.pdbj.org/ftp/pub/bmrb/metabolomics/entry_lists/xml/

BMRB/XML (noatom):

Master (BMRB+Metabolomics)
http://bmrbpub.protein.osaka-u.ac.jp/archive/xml-noatom/
BMRB
http://bmrb.pdbj.org/ftp/pub/bmrb/entry_lists/xml-noatom/
Metabolomics
http://bmrb.pdbj.org/ftp/pub/bmrb/metabolomics/entry_lists/xml-noatom/

BMRB/RDF (RDF/XML):

Master (BMRB+Metabolomics)
http://bmrbpub.protein.osaka-u.ac.jp/archive/rdf/
BMRB
http://bmrb.pdbj.org/ftp/pub/bmrb/entry_lists/rdf/
Metabolomics
http://bmrb.pdbj.org/ftp/pub/bmrb/metabolomics/entry_lists/rdf/

BMRB/RDF (N-Triples):

Master (BMRB+Metabolomics)
http://bmrbpub.protein.osaka-u.ac.jp/archive/rdf-nt/
BMRB
http://bmrb.pdbj.org/ftp/pub/bmrb/entry_lists/rdf-nt/
Metabolomics
http://bmrb.pdbj.org/ftp/pub/bmrb/metabolomics/entry_lists/rdf-nt/

BMRB/JSON (noatom):

Master (BMRB+Metabolomics)
http://bmrbpub.protein.osaka-u.ac.jp/archive/json-noatom/
BMRB
http://bmrbpub.protein.osaka-u.ac.jp/archive/json-noatom/mmcif_nmr-star-v3.2.0.9/bmr_json_noatom_doc/
Metabolomics
http://bmrbpub.protein.osaka-u.ac.jp/archive/json-noatom/mmcif_nmr-star-v3.2.0.9/bms_json_noatom_doc/

Protein Blocks annotation (NMR structure):

http://bmrbpub.protein.osaka-u.ac.jp/archive/pb/

Protein Blocks annotation (Related X-ray structure):

http://bmrbpub.protein.osaka-u.ac.jp/archive/pb_xray/

FASTA sequence (BMRB):

http://bmrbpub.protein.osaka-u.ac.jp/archive/fasta/

FASTA sequence (PDB):

http://bmrbpub.protein.osaka-u.ac.jp/archive/fasta_pdb/

FASTA sequence (EMDB):

http://bmrbpub.protein.osaka-u.ac.jp/archive/fasta_emdb/

BLAST database (BMRB):

http://bmrbpub.protein.osaka-u.ac.jp/archive/blastdb/

BLAST database (PDB):

http://bmrbpub.protein.osaka-u.ac.jp/archive/blastdb_pdb/

BLAST database (EMDB):

http://bmrbpub.protein.osaka-u.ac.jp/archive/blastdb_emdb/

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

http://bmrbpub.protein.osaka-u.ac.jp/archive/blastout/

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

http://bmrbpub.protein.osaka-u.ac.jp/archive/blastout_pdb/

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

http://bmrbpub.protein.osaka-u.ac.jp/archive/blastout_emdb/

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

http://bmrbpub.protein.osaka-u.ac.jp/archive/blastout_uniprotkb/

Completeness of assigned chemical shifts:

http://bmrbpub.protein.osaka-u.ac.jp/archive/cs_complete/
Excluded atoms from calculation of the completeness:
http://bmrbpub.protein.osaka-u.ac.jp/archive/cs_complete/excluded_atoms.str

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

http://bmrbpub.protein.osaka-u.ac.jp/archive/pdb_molprobity/oneline_files

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

http://bmrbpub.protein.osaka-u.ac.jp/archive/pdb_molprobity/residue_files

nmrML (FID) of BMRB metabolomics entries:

http://bmrbpub.protein.osaka-u.ac.jp/archive/bms-nmrml/

BMRB/XML (complete):

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/bmrb-xml .

BMRB/XML (noatom):

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/bmrb-xml-noatom .

BMRB/RDF: (RDF/XML)

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/bmrb-rdf .

BMRB/RDF (N-Triples):

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/bmrb-rdf-nt .

BMRB/JSON (noatom):

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/bmrb-json-noatom .

Protein Blocks annotation (NMR structure):

% rsync -avz --delete rsync://bmrbpub.protein.osaka-u.ac.jp/pb .

Protein Blocks annotation (Related X-ray structure):

% rsync -avz --delete rsync://bmrbpub.protein.osaka-u.ac.jp/pb-xray .

FASTA sequence (BMRB):

% rsync -avz --delete rsync://bmrbpub.protein.osaka-u.ac.jp/fasta .

FASTA sequence (PDB):

% rsync -avz --delete rsync://bmrbpub.protein.osaka-u.ac.jp/fasta-pdb .

FASTA sequence (EMDB):

% rsync -avz --delete rsync://bmrbpub.protein.osaka-u.ac.jp/fasta-emdb .

BLAST database (BMRB):

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/blastdb .

BLAST database (PDB):

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/blastdb-pdb .

BLAST database (EMDB):

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/blastdb-emdb .

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

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/blastout .

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

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/blastout-pdb .

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

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/blastout-emdb .

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

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/blastout-uniprotkb .

Completeness of assigned chemical shifts:

% rsync -avz --delete rsync://bmrbpub.protein.osaka-u.ac.jp/cs-complete .

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

% rsync -avz --delete rsync://bmrbpub.protein.osaka-u.ac.jp/molprobity-oneline .

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

% rsync -avz --delete rsync://bmrbpub.protein.osaka-u.ac.jp/molprobity-residue .

BMRB PostgreSQL 10 dump file (noatom):

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

Update:
% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/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:
http://bmrbpub.protein.osaka-u.ac.jp/schema/mmcif_nmr-star.dic.schema

nmrML (FID) of BMRB metabolomics entries:

% rsync -av --delete rsync://bmrbpub.protein.osaka-u.ac.jp/bms-nmrml .

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, 1-4 (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, open access, 1-8 (2017)

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, G√ľnther 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, ePub ahead, (2017)

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