Biological Magnetic Resonance Data Bank
A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
BMRB Deposition Systems
Notice: effective 6 February 2013 constraints and chemical shifts data deposited at PDB will be released at the same time the atomic coordinates are released.
Beta ADIT-NMR deposition system for depositing NMR data (not structures) to BMRB.
ADIT-NMR deposition system allows you to deposit at both PDB and BMRB.
BMRB accepts the following kinds of data:
SMSDep: Small Molecule Structure Deposition system.
Only those structures which are too small for the PDB to accept may be deposited here. Please read the PDB entry requirements page for the precise purpose and criteria for the SMSDep system.
The prefered file format for NMR data files is NMR-STAR, a Self-defining Text Archival and Retrieval format (STAR). STARch is a software tool that can convert data files from various formats, including PIPP, XEASY, and tab-delimited files generated from common spreadsheets into NMR-STAR format.
Individual data files along with the information you enter about your study will be collated into a single NMR-STAR file. An excellent example of an NMR-STAR file with a number of types of data is entry 4267: Apo-HNGAL Human Neutrophil Gelatinase-Associated Lipocalin.
Time domain data (raw spectral data) is uploaded separately via ftp. Please see the instructions on how to upload time domain data.
To submit additional or corrected data for an existing BMRB entry, please send the file(s) as e-mail attachment to BMRB annotators: email@example.com, or to BMRB help alias: firstname.lastname@example.org
Pre-deposition data validation services
Chemical Shift vs Coordinate nomenclature check A tool to check Assigned Chemical Shift nomenclature versus Coordinate file nomenclature. This tool runs the same checks as will be run later when you deposit atomic coordinates with ADIT-NMR.
Protein Structure Validation Suite (PSVS) is a useful tool for the assesment of protein structures generated by NMR and X-ray methods. PSVS is broadly applicable for structure quality assessment in structure biology projects.
iCing Validation Package is part of the Common Interface for NMR structure Generation (CING) package.
CheckShift - Chemical Shift Reference Check at Center of Applied Molecular Engineering, the University of Salzburg, Austria. It works on NMR-STAR 2.1, SHIFTX or TALOS files.
Format conversion tools
STARch file converter: converts data files in various formats to NMR-STAR 3.1 for upload to ADIT-NMR.
NMR-STAR template generator: produces NMR-STAR 3.1 formatted tables for NMR data.
Ambiguity code assignment interface: simplifies assignment of chemical shift ambiguity codes.
NMR-STAR to other formats: converts NMR-STAR 3.1 chemical shift tables to Sparky, NMRPipe/TALOS, XEASY, or NMR-STAR 2.1.Conversion tools donated by the NMR community
tab2bmrb: convert chemical shift tables between publication format and NMR-STAR 2.1 format. Also included are tools to calculate random coil chemical shifts and NMR experimental pulse lengths for experiments dependent on 3JHN(CA)HA coupling constants.
FELIX to NMR-STAR: software for converting FELIX chemical shift files to NMR-STAR 2.1 format.
PIPP to NMR-STAR: software for converting PIPP chemical shift files to NMR-STAR 2.1 format.
NMR-STAR to TALOS+: script for converting chemical shift tables in BMRB entries to TALOS+ input files.
CYANA to XPLOR: script for converting CYANA formatted files to XPLOR/CNS/PDB files.
Reference information about atom nomenclature, standard chemical shifts, indirect chemical shift references, etc.
Submitting pulse programs.
ASCII text files containing pulse sequences, text files describing the experiments, and other ancillary files can be submitted by anonymous ftp to "deposit.bmrb.wisc.edu". Please place the files in the incoming/pulse_sequence directory and notify BMRB by e-mail (email@example.com) that a pulse sequence has been deposited. Please indicate in the e-mail the names of all the files included in the submission.
This information can be included as comments in the file containing the pulse sequence.
Submitting software and macros.
ASCII text files containing the software macro can be submitted by anonymous ftp to "deposit.bmrb.wisc.edu". Please place the files in the incoming/macro_definition directory and notify BMRB by e-mail (firstname.lastname@example.org) that a program macro has been deposited. Please include the following information in the e-mail:
The above information can be included as comments in the file containing the macro.