[3dem] wwPDB NMR restraint remediation conforms to standard NMR-STAR and NEF format

[Justin Flatt]

NMR data files are standardized in NEF 
<https://urldefense.com/v3/__https://www.nature.com/articles/nsmb.3041__;!!Mih3wA!FOrzbXSA0z_kggNq1qO39shshP1xk-vZGsuuabtOxeunz5bSSl0ksb_o_jMI-OwOEnlRx_Iwd55HAxhC9hYljBOT$ > [1] and NMR-STAR format 
[Ulrich, 2019 
<https://urldefense.com/v3/__https://link.springer.com/article/10.1007/s10858-018-0220-3__;!!Mih3wA!FOrzbXSA0z_kggNq1qO39shshP1xk-vZGsuuabtOxeunz5bSSl0ksb_o_jMI-OwOEnlRx_Iwd55HAxhC9kXOCxAp$ > [2]] for 
the PDB entries which have NMR data in many different software specific 
formats. This remediation project provides unified NMR data in single 
NMR-STAR/NEF file for the PDB entries. wwPDB is moving forward single 
file upload for NMR data (restraints, chemical shifts and possibly peak 
list) in NMR-STAR/NEF format and will eventually phase out the upload of 
software specific format in OneDep in future. During transition period, 
OneDep converts certain restraint formats into NMR-STAR/NEF at the 
deposition and provides users with NMR restraint validation 
<https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2020*5fc8e8ab09ae2a096d081e27__;Iw!!Mih3wA!FOrzbXSA0z_kggNq1qO39shshP1xk-vZGsuuabtOxeunz5bSSl0ksb_o_jMI-OwOEnlRx_Iwd55HAxhC9uJLAeog$ > [3] 
in wwPDB validation reports for NMR entries having assigned chemical 
shifts and reasonable restraints in following supported formats:

AMBER, BIOSYM, CHARMM, CNS, CYANA, DYNAMO/TALOS/PALES, GROMACS, ISD,
ROSETTA, SYBYL, and XPLOR-NIH

Depending on complexity of restraints and whether spectral peak lists 
have been deposited, the first rollout includes NMR entries with simple 
restraints in the supported formats and without spectral peak lists. The 
next rollout will include entries with spectral peak lists. Entries 
which met the following criteria are the scope for remediation:

* Both assigned chemical shifts and restraints have been deposited to
the PDB
* A valid topology file or specific comments must be present to
interpret restraint files in a specific format (i.e. AMBER, CHARMM,
GROMACS)
* All atoms described in NMR data (assigned chemical shifts and
restraints) are consistent with model's atoms
* Sequence alignment between the model and restraints matches,
allowing terminal sequence extensions

NMR-STAR format is the master format used to handle wide variety of 
restraints in this NMR restraint remediation project. Data items 
starting with "Auth_asym_ID", "Auth_seq_ID", "Auth_comp_ID", and 
"Auth_atom_ID" terms, i.e. "_Gen_dist_constraint.Auth_seq_ID_1", point 
to equivalent data items in mmCIF, "_atom_site.auth_asym_id", 
"_atom_site.auth_seq_id", "_atom_site.auth_comp_id", 
"_atom_site.auth_atom_id", respectively. Complete atom name mapping 
information is incorporated using "_Assembly" and "_Entity" categories. 
NMR constraints used by structure determination software but not covered 
by the NMR-STAR ontology, such as chemical planarity, equilibrium bond 
angle, non-crystallographic symmetry, etc., are stored as JSON data 
under "_Other_constraint_list.text_data" tag to ensure no information is 
lost during remediation. Furthermore, statistics on remediated 
restraints are available. NEF data files are provided as best effort 
conversions from the master NMR-STAR data files.

New unified NMR data files in NEF and NMR-STAR formats of existing NMR 
entries are distributed in the "nmr_data" directory of the PDB archive 
in the same manner for entries accompanied by the single NMR data file 
(https://urldefense.com/v3/__https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_data/__;!!Mih3wA!FOrzbXSA0z_kggNq1qO39shshP1xk-vZGsuuabtOxeunz5bSSl0ksb_o_jMI-OwOEnlRx_Iwd55HAxhC9kf9KvXS$ ) and 
at BMRB archive 
(https://urldefense.com/v3/__https://bmrb.io/ftp/pub/bmrb/nmr_pdb_integrated_data/coordinates_restraints_chemshifts/remediated_restraints__;!!Mih3wA!FOrzbXSA0z_kggNq1qO39shshP1xk-vZGsuuabtOxeunz5bSSl0ksb_o_jMI-OwOEnlRx_Iwd55HAxhC9k6jogpH$ ). 
The existing data files in the PDB archive directories 
"nmr_chemical_shifts" and "nmr_restraints" are remained as is.

To retrieve NMR data, users should primarily obtain unified NMR data 
files at ../nmr_data directory. Conventional chemical shifts and 
restraints can be used only if unified NMR data are not available.

For newly deposited NMR entries with conventional separated NMR data 
files, OneDep now unifies assigned chemical shifts and restraints into a 
single data file, which can be accessed from OneDep upload summary page. 
After submission, depositors can not roll back to the conventional 
formats.

wwPDB validation reports are re-calculated to provide NMR restraint 
validation for the target entries. NMR restraints can be interpreted and 
weighted differently by various software during structure calculation. 
The NMR restraints validation software employs a more general approach 
recommended by NMR-VTF, independently verifying the satisfaction of each 
restraint in every model. This can occasionally result in a large number 
of violations when the actual structure determination software adopts a 
different approach or assigns less weight during structure calculation.

For any further information about NMR data remediation, please contact 
us at deposit-help at mail.wwpdb.org.

See wwPDB news at 
https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2023*64875a3cd78e004e766a967c__;Iw!!Mih3wA!FOrzbXSA0z_kggNq1qO39shshP1xk-vZGsuuabtOxeunz5bSSl0ksb_o_jMI-OwOEnlRx_Iwd55HAxhC9qqQVjeK$ .



Links:
------
[1] https://urldefense.com/v3/__https://www.nature.com/articles/nsmb.3041__;!!Mih3wA!FOrzbXSA0z_kggNq1qO39shshP1xk-vZGsuuabtOxeunz5bSSl0ksb_o_jMI-OwOEnlRx_Iwd55HAxhC9hYljBOT$ 
[2] https://urldefense.com/v3/__https://link.springer.com/article/10.1007/s10858-018-0220-3__;!!Mih3wA!FOrzbXSA0z_kggNq1qO39shshP1xk-vZGsuuabtOxeunz5bSSl0ksb_o_jMI-OwOEnlRx_Iwd55HAxhC9kXOCxAp$ 
[3] https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2020*5fc8e8ab09ae2a096d081e27__;Iw!!Mih3wA!FOrzbXSA0z_kggNq1qO39shshP1xk-vZGsuuabtOxeunz5bSSl0ksb_o_jMI-OwOEnlRx_Iwd55HAxhC9uJLAeog$ 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20230614/7b3dbd5e/attachment.html>