Worldwide Protein Data Bank symposium in Cold Spring Harbor
The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is organising a scientific
symposium in Cold Spring Harbor this autumn to celebrate the 40th anniversary
of the inception of the PDB and the many scientific contributions it archives.
The meeting ("PDB40") will kick off with an evening reception and plenary
session on Friday 28 October and conclude after lunch the following Sunday. For
details and registration, please see the meeting website at:
The program will showcase the scientific impact made by structural biology
during the past 40 years with a distinguished panel of scientists who have been
instrumental in the development of the PDB and structural biology. A list of
all confirmed speakers and the titles of their presentations is now on the
website.
May 31, 2011
S2 Predicted vs. Experimental Visualizations
We have added visualizations of S2 predicted vs. experimental
values to the available visualizations for BMRB entries.
(Predicted values are determined from the relevant PDB structure
by
s2predict.)
S2 predicted vs. experimental visualizations are currently
available for the following entries:
For entries for which this visualization is available, you can
view it by simply selecting the appropriate link in the
visualization summary page.
March 14, 2011
Two-Entry Visualizations
We have released a new version of the Peptide-CGI visualization
generation tool that allows the creation of visualizations
incorporating data from two entries (or data uploaded to the
visualization server and a released entry). At the present time,
the two-entry visualizations available are the simulated 1H-15N
backbone HSQC spectrum and the simulated 1H-13C HSQC spectrum
(more visualizations are planned). It is not yet possible to
generate visualizations combining two visualization server
data sets.
You can access the two-entry visualizations in two ways:
On the visualization summary page for each entry (or
visualization server data set), there is a form that allows
you to enter an accession number, which is then visualized in
combination with the current entry.
Note that, to compare uploaded data with a released entry, you
must first upload your data to the
visualization server and generate the single-data set
visualizations. At that point, you can specify an entry to
compare with your data.
For an example using entries 16606 and 16607, click
here.
November 10, 2010
Announcement: Chemical Shift Data Required for NMR Depositions Starting December 6, 2010
Effective December 6, 2010, deposition of chemical shift data will be mandatory when submitting NMR entries to the PDB.
These data must be deposited at a member site of the
Worldwide Protein Data Bank:
BMRB,
PDBj-BMRB,
PDBe,
RCSB PDB, or
PDBj.
Data can be released as soon as they have been processed and approved.
There is a one-year limit on the length of time a structure and its experimental data can be put on hold,
including structures that are on hold until the associated paper is published (HPUB).
This policy was developed as a result of comments and recommendations from the PDB user community,
including the NMR Task Force, and has been endorsed by the wwPDB Advisory Committee.
Changes to wwPDB Deposition Systems
New versions of the ADIT-NMR deposition system (BMRB and PDBj-BMRB) and AutoDep (PDBe)
have been developed to support the new chemical shift deposition requirement.
These systems will support the deposition of chemical shift data in NMR-STAR (V3.1)
format and will perform checks to confirm the correspondence between the atom
nomenclature in the chemical shift and coordinate data files.
AutoDep (PDBe) will also accept depositions containing chemical shifts from CCPN projects.
Additional tools are provided to assist depositors in preparing and pre-checking
chemical shift data prior to deposition: various data validation services are available at BMRB and PDBj-BMRB
(http://www.bmrb.wisc.edu/validate/ or
http://bmrb.protein.osaka-u.ac.jp/validate/)
and at PDBe including the FormatConverter
(http://www.ebi.ac.uk/pdbe-apps/nmr/software/formatConverter.html)
and standalone tools to generate deposition ready CCPN projects from more conventional data.
Changes to wwPDB FTP Server
NMR chemical shift data files will be added to the wwPDB ftp site with each weekly release.
Chemical shift data files will be named "1abc_cs.str.gz", where "str" identifies the NMR-STAR (V3.1) data format.
All chemical shift data files will be compressed (.gz) using the GNU gzip program.
Chemical shift files will be stored in a new directory path, grouped by the middle two characters of the 4-character PDB ID:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/nmr_chemical_shifts/. All of these data files will be symbolically linked to a single directory:
ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/nmr_chemical_shifts/.
In addition, the chemical shift data will be processed and included as entries in the BMRB archive.
Questions relating to depositions should be sent to info@wwpdb.org.
July 13, 2010
Easier Visualization Switching in DEVise
We have released a new version of the DEVise visualization tool that
allows users to switch visualizations within the DEVise applet. (Note
that, as part of this change, visualizations now appear in a new window,
rather than embedded within the browser window.)
To switch between available visualizations for a given entry, select
Session->Open/Switch in the DEVise applet. This will show a dialog
listing the visualizations that are currently available for the current
entry. Note that some visualizations (such as coordinates and restraints)
require additional processing on the server, so you may have to go back
to the "all visualizations" page for the entry to access them. Also,
if you switch visualizations inside the JavaScreen, the "help on this
visualization" link will no longer correspond to the visualization you
are viewing.
This functionality is currently not available within the visualization
server where users can upload data from their local computer and obtain
a visualization of the data.
July 12, 2010
Visualizations of distance restraints and their violations
We have added visualizations of distance restraints to the available
visualizations for BMRB entries. The visualizations consist of distance
restraint data (from the restraints grid, with violations calculated by
CING, or from the remediated restraints), combined with coordinates
from the PDB entry, producing integrated visualizations of the distance
restraint data and the 3D structure. The distance restraint data can
also be visualized based on PDB ID, rather than BMRB accession number
(see the BMRB search page at http://www.bmrb.wisc.edu/search/).
For more detailed information, see the visualization help page
here.
July 9, 2010
NMR derived binding data now archived in BMRB entries
BMRB entries containing
binding constants (Kd) and reaction rate constants (kon and koff)
extracted from the peer-reviewed literature are now being released to the
public. A link, Binding Data,
on the BMRB homepage provides access
to a webpage with the full list of entries and links to individual
entries. NMR spectroscopists, who are publishing these kinds of data, are
strongly encouraged to deposit their results at BMRB.
May 6, 2010
wwPDB To Provide Validation Reports as PDFs
As part of the structure annotation process, wwPDB members provide depositors with detailed reports that include the results of geometric and experimental data checking. Beginning May 17, 2010, these documents will be available from all wwPDB annotation sites as PDF files so that they may be easily reviewed and shared by depositors.
Version 2 NMR Restraint Files to be Released in the wwPDB FTP
With the June 30, 2010 update, a new set of NMR restraint data files will be added to the wwPDB FTP archive. These restraint files, which will be identified as Version 2 files, are represented in NMR-STAR 3.1 format, contain current PDB atom nomenclature, and provide accurate atom-level correspondences to the NMR model coordinate files in the current wwPDB archive. Restraint files containing restraint data as originally deposited (Version 1 files) will remain on the site and will continue to be updated regularly as new NMR entries are released.
Files are named merged_BMRB-ID_PDB-ID.str and entry IDs in the files
follow the pattern: cBMRB-ID_PDB-ID. For example, the file
merged_10141_2e9g.str combines data from BMRB entry 10141 and PDB entry 2e2g, and
has internal entry ID c10141_2e2g.
February 9, 2010
BMRB FTP site reorganization
We have moved and renamed various files and directories on the
BMRB FTP site (also available over HTTP via
FTP Access page). The new site comes with better directory layout
and more descriptive file names.
Note that names and locations of some files have changed. In particular,
the file containing the list of matching PDB and BMRB entries is now
adit_nmr_matched_pdb_bmrb_entry_ids.csv, located in nmr_pdb_integrated_data
directory of the BMRB section of the site.
February 3, 2010
Torsion angle restraint visualizations
We have added visualizations of torsion angle restraints, and their
violations, to the available visualizations for BMRB entries. The
visualizations consist of torsion angle restraint data (from the
restraints grid, with violations calculated by CING), combined with
coordinates from the PDB entry, producing integrated visualizations of
the torsion angle restraint data and the 3D molecule. The torsion angle
data can also be visualized based on PDB ID, rather than BMRB accession
number (see the search page). For more detailed information, see the
visualization help page.
December 21, 2009
We have added a CS-Rosetta structure calculation
service to the BMRB website. Users can upload chemical shift files and run the protein structure prediction software
CS-Rosetta on a
CONDOR high-throughput computing cluster.
December 8, 2009
Visualization tutorial videos
We have developed two tutorial videos on the use of the DEVise/JavaScreen web-based
visualization tool at the BioMagResBank web site. The subjects of the tutorials are as follows:
Tutorial 1 covers DEVise cursors, zooming, the most important toolbar modes (drill down,
cursor fill, home, and view help), accessing the JavaScreen help page, and how to access
visualizations at BMRB.
Tutorial 2 covers the BMRB visualization summary page for each entry, the rest of the toolbar
modes (zoom modes, axis range toggle, and symbol enlarge/reduce), and session restart, axis
range reset, display (color) modes, and communication modes (normal and CGI).
We hope that these tutorials will make it easier for users to fully take advantage of the
capabilities of the JavaScreen visualization tool.
We plan to create more tutorials, covering topics such as the 3D interface in the JavaScreen
and the use of the visualization server at BMRB.
Time domain data links inserted into BMRB NMR-STAR files
Links to time domain data have been incorporated into the NMR-STAR v3.1 files for 106 BMRB entries
(ftp://ftp.bmrb.wisc.edu/pub/bmrb/timedomain_entries/).
This includes links to the raw spectral data that was processed and analyzed to produce assigned
chemical shifts and constraints for structure calculations. Links for pulse programs, acquisition
parameters, processing parameters, and peak lists are also included in the entries for many NMR
experiments. This information can be used to develop new methods of automatic structure calculation,
peak assignment, and analysis.
June 10, 2009
Beta NMR-STAR table converter tool
NMR-STAR 3.1 table converter is available for beta testing at
http://pike.bmrb.wisc.edu/software/conv/index2.html.
The tool can convert assigned chemical shifts table to XEASY, TALOS, and Sparky formats. It can
also convert most NMR-STAR 3.1 data tables (not just chemical shifts) to NMR-STAR 2.1.
There is now a new page on the BMRB web site highlighting the various validation tools that
can be used by depositors. This page was created in response to requests that validation
tools be more accesible to depositors. The BMRB strongly encourages pre-deposition
validation of NMR experimental data and structure files.
December 19, 2008
Ambiguity code assignment interface
A web-based program for assigning chemical shift ambiguity codes
is available in the Deposit section of BMRB website. The program finds potentially
ambiguous chemical shift assignments in an NMR-STAR 3.1 table and asks which are unique.
The output is an NMR-STAR 3.1 table with ambiguity codes filled in.
July 30, 2008
Small molecule entries on the FTP site
Several small molecule structure entries (entry IDs in the 20000 range) have been released
and are available from entry files directory on
the FTP site. Each entry directory contains NMR-STAR files in both v.3 and v.2.1 formats,
coordinate file, constraint file(s), and, if available, AVS report file.
We are working on adding these to the entry summary webpage.
March 20, 2008
NMR-STAR V3 Files on FTP site
BMRB has released several of the entries as NMR-STAR version 3 files here:
For those in the NMR community wishing to see a preview of what NMR-STAR version 3
files will be like for the purpose of adapting software or reviewing the
format, this archive provides a list of clean examples from recent entries.
Recent entries have been annotated entirely in NMR-STAR version 3, and converted
back to version 2 for publication on the website. These files provide a view
of what the entries contain before being converted back to version 2. In the
future, all entries on the BMRB website will be in NMR-STAR version 3 by default
(with a link to the NMR-STAR version 2 files so they may be obtained for
backward compatibility).
Although NMR-STAR version 3 will become the default way entries are published on
the BMRB website, all entries, new and old, will have both a version 2 and a version 3 copy
available on the site. This is for backward compatibility with software written
for NMR-STAR version 2.
Please try it out and contact us with any
comments and suggestions.
April 20, 2007
Chemical Shift Query
BMRB has released a
Chemical Shift Query tool.
The tool allows you to
create tables of chemical shift information by specifying the residue of
a protein or nucleic acid. The search query can encompass the entire
database, or be limited by BMRB entry, atom name, or range of chemical
shifts. The results can be viewed directly on the web page or downloaded
as a tab-separated file that can be viewed in a text editor or
spreadsheet such as Microsoft Excel.
Please try it out and contact us with any
comments and suggestions.
