[ccp4bb] Beta Test the Next Generation RCSB PDB website at http://beta.rcsb.org

[Christine Zardecki]

Test drive significantly revised and updated tools for searching and exploring 
PDB data at http:// <http://beta.rcsb.org/>beta.rcsb.org 
<http://beta.rcsb.org/> before this new site is moved into production in April.
Improved and enhanced tools include:

Basic Search available from the search box at the top of every page
Advanced Search Boolean options 
Display of Advanced Search results for PDB structures, assemblies or unique 
polymeric molecular entities (unique sequences)
Structure and Sequence Similarity and Annotation Browsing integration in 
Advanced Search
Left-hand menu for refining Search Results 
Stored Search History
New MyPDB features: registration via Google/Facebook/ORCID authentication; 
save/rerun/receive email notifications of searches
Improved Download Tool for batches of data files
New GraphQL and REST APIs for data access and searching
Please note some RCSB PDB features are still in development but will be made 
available soon, including Custom Tabular Reports and a Chemical Component 
Search tool.

Your feedback will help ensure RCSB PDB services support our users. Please use 
the orange Contact Us button on the middle of the right-hand side of each page.



------
CHRISTINE ZARDECKI
Deputy Director, RCSB Protein Data Bank
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4924 | E: christine.zarde...@rcsb.org 
<mailto:christine.zarde...@rcsb.org>





To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Due Aug 1: PDB40 Travel Award Applications for Early Career Scientists and Students

[Christine Zardecki]

Celebrate four decades of innovation in structural biology this fall at a Cold 
Spring Harbor Laboratory symposium honoring the PDB's 40th anniversary and the 
many scientific contributions it archives.

TRAVEL AWARDS
Limited funds are available to help students and early career scientists attend 
PDB40. Preference will be given to those who have submitted poster abstracts. 
To apply for assistance, download the application form from the PDB40 website, 
and email the completed form, a copy of your abstract, and a supporting letter 
from your research advisor/department chairman to i...@wwpdb.org. Funds are 
non-transferable. Awards will be distributed after the meeting. Applications 
are due by August 1, 2011. 

POSTERS
The meeting will also host a session of poster presentations. To submit your 
abstract for consideration, please submit online following the link provided 
after registration. The status of abstracts will be posted as soon as decisions 
have been made by the organizers.  The deadline for poster submission is August 
15, 2011. 

GENERAL INFORMATION
PDB40, organized by the Worldwide Protein Data Bank (wwPDB), will begin with an 
evening reception, dinner, and oral session on Friday, October 28th and 
conclude with lunch on Sunday, October 30, 2011. 

Early registration is strongly encouraged as the meeting is expected to fill 
quickly. For complete meeting details, see 
http://meetings.cshl.edu/meetings/pdb40.shtml. 

SPEAKERS
Cheryl Arrowsmith (University of Toronto, Canada)
David Baker (University of Washington) 
Ad Bax (NIH/DHHS/NIDDK/LCP) 
Axel Brunger (Stanford University/HHMI) 
Stephen K. Burley (Eli Lilly & Co.) 
Wah Chiu (Baylor College of Medicine) 
Angela Gronenborn (University of Pittsburgh) 
Richard Henderson (MRC Lab. of Molecular Biology, UK) 
Wayne Hendrickson (Columbia University) 
Mei Hong (Iowa State University) 
So Iwata (Imperial College London, UK) 
Louise Johnson (University of Oxford, UK) 
T. Alwyn Jones (University of Uppsala, Sweden) 
Brian Matthews (University of Oregon) 
Jane Richardson (Duke University Medical Center) 
Michael Rossmann (Purdue University) 
Andrej Sali (University of California, San Francisco) 
David Searls (Independent Consultant) 
Susan Taylor (University of California, San Diego) 
Janet Thornton (EMBL, Hinxton, UK) 
Soichi Wakatsuki (IMMS-KEK, Japan)   
Kurt Wüthrich (The Scripps Research Institute/ETH Zürich) 

--
Like the Worldwide Protein Data Bank on Facebook: http://on.fb.me/l3m9qT

Re: [ccp4bb] Another paper & structure retracted

[Christine Zardecki]

A few words on obsoleted entries and validation reports:

OBSOLETE ENTRIES

Obsolete entries remain available to the public through the PDB ftp archive at 
ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/. 

For example, for entry 1F83, you can access the coordinate file at 
ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/pdb/f8/pdb1f83.ent.gz  and 
the structure factors at 
ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsolete/structure_factors/f8/r1f83sf.ent.gz.

If there is a superceding entry, many websites that serve PDB data will 
automatically redirect you to the superceding entry. 

In the rare cases when a journal retracts a publication, and the reason(s) for 
retraction were such that the associated PDB entry needs to be made obsolete, 
wwPDB will obsolete the entry. The retraction will be listed as the citation in 
the obsoleted file. The entries described in recently retracted publications 
(3O8K and 2QNS) will be subjected to this process. This is a recent change to 
wwPDB policy - historically, the reasons for making PDB entries obsolete 
(without superceding them) have not been captured.

Current wwPDB policy describing the process is at 
http://www.wwpdb.org/policy.html#toc_changes

VALIDATION REPORTS
--
The wwPDB encourages authors of structure papers to submit, and journal editors 
and referees to request, PDB Validation Reports as part of the manuscript 
submission and review process. 

As part of structure annotation, wwPDB deposition sites produce reports that 
include the results of geometric and experimental data checking. These reports 
provide a basic assessment of structure quality while keeping the coordinate 
file confidential.

The validation reports will continue to be developed and improved as we receive 
recommendations from the wwPDB Validation Task Forces (VTFs) for X-ray, NMR and 
3DEM and as we further develop our data deposition and processing procedures. 
The X-ray VTF recommendations will be published soon, with white papers by the 
NMR and EM VTFs to follow. 

PDB validation reports are already required by the International Union of 
Crystallography (IUCr) journals as part of their submission process 
(http://journals.iucr.org/d/services/submitinstructions.html#supplement) and 
are described in an editorial published in Nature Structural & Molecular 
Biology (http://www.nature.com/nsmb/journal/v17/n8/full/nsmb0810-917.html).



Christine Zardecki
for the wwPDB


--
PDB 40: Celebrate four decades of innovation in structural biology
Oct 28-30, 2011 at Cold Spring Harbor Laboratory
http://meetings.cshl.edu/meetings/pdb40.shtml

Like the Worldwide Protein Data Bank on Facebook: http://on.fb.me/l3m9qT

Re: [ccp4bb] _diffrn.detail in PDB sf.cif releases

[Christine Zardecki]

This is an error that will be corrected; we'll also fix the source of  
the problem so that it won't appear again.


Thanks to Tom Womack for bringing this to our attention.

Questions and comments for the wwPDB about data files and formats may  
also be sent i...@wwpdb.org.


Christine
for the wwPDB





From: Thomas Womack 
Date: March 3, 2010 6:24:38 AM EST
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] _diffrn.detail in PDB sf.cif releases
Reply-To: Thomas Womack 


I notice that a fair number of PDB-deposited sets of structure  
factors in sf.cif format (fourteen of them in the March 2 2010  
release) contain an _diffrn.detail line; this comes to my attention  
because ccp4-6.1.2's cif2mtz falls over when it encounters such a  
line and I have to edit the CIF manually to get it to continue.


I have never observed this line to have a value other than '?'; is  
it known what software produces sf.cif files with this meaningless  
and problematic line in, and how to make it stop?


http://mmcif.rcsb.org/dictionaries/mmcif_pdbx.dic/Categories/ 
diffrn.html


does not mention _diffrn.detail, although it offers an optional  
_diffrn.details line, and one example where that was used to  
describe a data-gathering protocol where exposure increased over time.


Tom

[ccp4bb] wwPDB Announcements: Validation Report PDFs, NMR Restraint Files

[Christine Zardecki]

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.


For more information, please see:
http://www.wwpdb.org/news.html#30-April-2010_1


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.


For more information, please see:
http://www.wwpdb.org/news.html#30-April-2010_2



Questions? Please contact i...@wwpdb.org. 

Re: [ccp4bb] Question: Refmac5 stats reported in pdb REMARK 3

[Christine Zardecki]

Dear Phil,

Your observation that the refinement details in PDB format REMARKs  
are difficult to interpret and compare is well taken. Each refinement  
package produces its own set of refinement results calculated in its  
own way. Both the calculation and presentation of this information in  
PDB format differs between programs, and even between program  
versions. The lack of standardization in how refinement information  
is reported is confusing to many PDB users.


In the spirit of supporting innovation, the PDB has historically  
tried to accommodate this diversity by providing program- and version- 
specific REMARK 3 formats.  However, the field of structural biology  
has matured considerably in the past few decades, and time-tested,  
consensus, and best-practice approaches can now be defined in many  
cases. In our view, adopting such approaches (rather than  
accomodating every variant ever implemented) would be the best way to  
serve the interests of both non-expert user communities and the  
experimental structural biology community.


As an illustration, it is interesting to note that there are at least  
20 different types of R-values reported in the current archive. The  
subtle differences in these quantities may be of interest in  
understanding the evolution of refinement methodology. However, we  
believe that a smaller, common set of well-defined data items  
describing refinement results would be more useful to the broader  
community of PDB users.


To this end, the wwPDB maintains an Exchange Data Dictionary of  
community-vetted definitions and examples of each data item in the  
PDB archive. This is an extensible dictionary that grows with new  
technologies and science. For instance, wwPDB has used this  
extensibility to capture and define all the various R-values. While  
the dictionary technology provides a framework for definition and  
standardization, this only addresses part of the problem.


Even though we have precise definitions for the wide range of R-value  
types, R-value comparisons  between entries is still complicated  
because the values are not uniformly populated across the archive. To  
fully address the problem, we not only need the standardization  
provided by the dictionary technology but also the cooperation of the  
software package developers in producing a common set of statistics  
and diagnostics. This does not preclude reporting new and novel data  
items, but these should be provided in addition to a common core of  
data results.


Further information about the PDB Exchange Data Dictionary can be  
found at our dictionary resource site, http://mmcif.pdb.org/


Correspondence information between our PDB Exchange Data Dictionary  
and items in the current PDB format is also available at

http://mmcif.pdb.org/dictionaries/pdb-correspondence/pdb2mmcif-2010.html

Sincerely,

Christine Zardecki
for the wwPDB




From: Phil Jeffrey 
Date: May 19, 2010 4:02:22 PM EDT
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question: Refmac5 stats reported in pdb REMARK 3
Reply-To: Phil Jeffrey 



Compare these two lines from phenix.refine:
REMARK   3   NUMBER OF REFLECTIONS : 46001
REMARK   3   FREE R VALUE TEST SET COUNT  : 2339

with those from refmac, ostensibly using the same data and start pdb:
REMARK   3   NUMBER OF REFLECTIONS :   43672
REMARK   3   FREE R VALUE TEST SET COUNT  :  2339


I know there are 46011 reflections with |F|>0 in the files I used.
phenix.refine removes 10 of these as outliers.  The 46001 remaining  
reported in REMARK 3 *include* the test set.


With REFMAC, 43672+2339=46011 so it appears that Refmac reports  
just the *working* set count in that first line, excluding the test  
set.


Is this is a bug with one program or the other, or a bug in the PDB  
definition of REMARK 3 ? http://www.wwpdb.org/documentation/ 
format23/remark3.html


This appears to be a source of inconsistency.

phenix.refine 1.6-289
refmac5 5.4.0077  (I'm apparently a Luddite)

Phil Jeffrey
Princeton

Re: [ccp4bb] Finding best model for molecular replacement

[Christine Zardecki]

Dear Paul,

A few options may be of interest:

RCSB PDB Sequence Searching:
Paste your sequence into the sequence search box at:
http://www.pdb.org/pdb/search/advSearch.do?st=SequenceQuery
(also available from Advanced Search and from the Sequence Search of  
the left hand menu).


Sequence search results are ordered by e-value.  Note, the sequence  
alignment on the results page comes from the BLAST output file. BLAST  
uses the sequence from SEQRES and the sequence numbering always  
starts at 1. The sequence numbers of the residues in the ATOM records  
may be different.


To see which part of an aligned sequence is actually present in a  
structure, go to the Structure Summary page for an entry and click on  
the Sequence tab.


PSI Structural Genomics Knowledgebase:
Paste your sequence into the search box at
http://kb.psi-structuralgenomics.org/
This search will return any related structures, models, targets,  
protocols, and materials.


MRBUMP (CCP4: Supported Program):
http://www.ccp4.ac.uk/MrBUMP/mrbump_doc.html
For a given target sequence, automated discovery of chains, domains  
and multimers that are possible templates for molecular replacement  
search models


Christine
RCSB Protein Data Bank





On 05/23/10 15:23, Paul Lindblom wrote:


Hi everybody,

I just crystallized a new project protein. How can I find a  
possible model for using molecular replacement? I have the  
sequence of my protein. Is it enough to make a sequence search in  
the pdb? Or is there another approach I can use?


Thanks a lot,

Paul

Re: [ccp4bb] Converting cif-files into pdb-files / reading cif -files into coot

[Christine Zardecki]

Hello,

The CIFTr program is a simplied mmCIF to PDB format converter that
can be downloaded at http://sw-tools.pdb.org/apps/CIFTr/index.html.

A more complete conversion, including remarks and other experimental
details, can be performed using the Maxit program.   This program can
be downloaded at at http://sw-tools.pdb.org/apps/MAXIT/index.html.

Best,

Christine



From: Vellieux Frederic 
Date: June 1, 2010 9:30:29 AM EDT
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Converting cif-files into pdb-files / reading  
cif -files into coot

Reply-To: Vellieux Frederic 


Hi Christian,

Had exactly the same problem (converting an mmCIF file into a PDB).  
I located and installed CIFTr . The version I have running here is  
ciftr-v2.053 . I am afraid I can't remember exactly where I  
downloaded it from.  I think it one of the PDB associated files.


Fred.

Christian Engel wrote:

Dear All,
 I am looking for a ccp4 program that reads in cif-files and  
converts them into pdb-files, including the CRYST1 card. Can  
anybody suggest a solution? I didn't find any in ccp4i, e.g. the  
coordinate utilities.
 I also tried COOT to read in cif-files (downloaded from the pdb  
server). For one example it crashed, for others it doesn't colour  
the bonds properly if "Bonds (Colour by Atom)"  is chosen but  
shows all bonds in one colour. Is that a known feature? If I save  
these coordinates in pdb-format and try to read it back, I get an  
ERROR saying: "Wrong ASCII format of an integer".

  Thanks for any suggestions
Christian Engel


*/Mit freundlichen Grüßen / Best regards / Cordialement/*

Dr. Christian Engel

Sanofi-Aventis Deutschland GmbH
R&D CAS Structural Biology FFM
Industriepark Hoechst
Bldg. G877, Room 020
D-65926 Frankfurt am Main
t: +49 69 305 12946
f: +49 69 305 80169
w:_www.sanofi-aventis.de_

125 Jahre Arzneimittel aus Deutschland von sanofi-aventis

 
* 
* 
***

Sanofi-Aventis Deutschland GmbH ·  Sitz der Gesellschaft:
Frankfurt am Main · Handelsregister: Frankfurt am Main, Abt. B  
Nr.

40661
Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschäftsführer:
Dr. Martin Siewert (Vorsitzender), Ulf Bialojahn, Dr. Matthias  
Braun,

Peter Guenter, Prof. Dr. Dr. Werner Kramer, Dr. Klaus Menken, Dr.
Heinz Riederer
 
* 
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[ccp4bb] Where to find "novelty" of PDBids?

[Christine Zardecki]

TargetDB performs this type of analysis for structures deposited by  
structural genomics projects.

Tabulations of novel depositions can be found at
http://targetdb.pdb.org/Metrics/MilestonesTables.html.

The data from which these statistics were calculated from sequence  
clustering performed by the RCSB PDB.  Sequence clustering is updated  
weekly at ftp://resources.rcsb.org/sequence/clusters/.


Archived, time-stamped files containing sequence clustering data from  
the weekly update from 2007 - 2009 are available from
ftp://snapshots.rcsb.org/20090105/pub/pdb/derived_data/NR/blastclust/ 
archive/.


Best,

Christine
RCSB Protein Data Bank

 Original Message 
Subject:
[ccp4bb] Where to find "novelty" of PDBids?
Date:
Wed, 9 Jun 2010 09:52:46 +0100
From:
Frank von Delft 
Reply-To:
Frank von Delft 
To:
CCP4BB@JISCMAIL.AC.UK


Hi, for an analysis I need the sequence identity of any PDBid to its
closest match in the PDB *at the time it was deposited*.

It seems like something somebody would have done before;  any thoughts
where to find it?

Cheers
phx

[ccp4bb] Improved Version of ADIT Available

[Christine Zardecki]

Improved Version of ADIT Available

An updated and enhanced version of ADIT is now available for  
depositing new entries at http://deposit-beta.rcsb.org/adit/. We  
encourage depositors to use this new tool and send feedback to  
depo...@deposit.rcsb.org.


ADIT is used to validate and submit structures to the PDB archive.   
Based upon user feedback, we have made improvements to the help  
statements and documentation provided. This version of ADIT indicates  
file format errors and provides suggestions for solutions;  
automatically runs validation checks; and reviews the consistency  
between sequence and coordinates. The forms for entering sequence  
information, structure title, author names, and citation information  
have also been improved.


Currently, this new version of ADIT is being transitioned into  
production, and will become the default site for deposition on  
selected days each week for testing. The date of full deployment will  
depend upon the results of this testing.


Deposition sessions currently in process will not be disrupted;  
depositors will not have to update any bookmarks or session ID. 

Re: [ccp4bb] LIGPLOT or similar

[Christine Zardecki]

Mark,

Ligand Explorer displays hydrogen bonds, water-mediated hydrogen  
bonds, metal coordination, and hydrophobic contacts. High resolution  
images can be exported in several file formats.


Ligand Explorer is available from each PDB entry's Structure Summary  
page at the RCSB PDB (www.pdb.org).


For examples:

* go to http://www.pdb.org/pdb/explore/explore.do?structureId=1STP
and launch Interaction View/Ligand Explorer from the Ligand/Chemical  
Component box


* launch the program directly from
http://www.pdb.org/pdb/explore/viewerLaunch.do? 
viewerType=LX&structureId=1OHR&hetId=1UN


In this URL, 1OHR specifies the PDB ID, and 1UN the Chemical  
Component ID.


Best,

Christine
RCSB PDB



On Wed, Aug 25, 2010 at 07:51:08PM +0200, Mark J van Raaij wrote:
> Dear All,
>
> Having just installed LIGPLOT under Windows, I find it rather  
convoluted to run. It has to be run via de command line window, and I  
try to avoid Windows as much as I can anyway.
> I also tried to install the Unix version on MacOSX, but was not  
able to get it running properly, probably at least partly due to my  
relative lack of informatics skills...

>
> Is there an alternative program that does the same (pref. with  
MacOSX version)?

>
> For the LIGPLOT developers, ideal would be a MacOSX installer  
(dmg) - I think it would lead to more use of your program.

>
> Greetings,
>
> Mark van Raaij

[ccp4bb] Announcement: Standardization of Amino Acid Nomenclature

[Christine Zardecki]

Announcement: Standardization of Amino Acid Nomenclature

The wwPDB is transitioning to use the nomenclature for pyrrolysine and 
selenocysteine as recommended by the joint nomenclature committee of 
IUPAC/IUBMB.

Starting in January, PYL (for pyrrolysine) and SEC (for selenocysteine) will be 
used where three-letter codes appear for amino acids in new releases and 
updated in entries currently in the archive (<50 entries).

In April, the letter O (for pyrrolysine) and U (for selenocysteine) will be 
used where one-letter codes appear for amino acids in new releases and updated 
in entries currently in the archive.

Questions and comments should be sent to i...@wwpdb.org. 

Re: [ccp4bb] 3D printing format

[Christine Zardecki]

The NIH 3D Print Exchange (http://3dprint.nih.gov/) has a collection of files 
for 3D printing, and can generate files based on PDB ID.

Christine
--
Twitter: http://twitter.com/#!/buildmodels
Facebook:  http://www.facebook.com/RCSBPDB

[ccp4bb] Celebrate PDB50 at the Inaugural May 4-5 Event (register by March 15)

[Christine Zardecki]

Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB 
archive (http://wwpdb.org/pdb50).

The inaugural symposium will be held virtually on May 4-5, 2021.  

The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day.  
The event will be recorded and made available to registered participants after 
the meeting.  

Students and postdoctoral fellows are especially encouraged to attend and will 
be eligible for poster awards.

Register at https://www.asbmb.org/meetings-events/pdb50 by March 15 for reduced 
rates.

Speakers

Using HIV-1 reverse transcriptase structures to guide anti-AIDS drug discovery
Edward Arnold, Rutgers, The State University of New Jersey

The evolution of the Protein Data Bank as a community resource
Helen M. Berman, Rutgers, The State University of New Jersey and University of 
Southern California

A personal history of five decades of structural biology and the PDB: From the 
X-ray structure of 2-Zinc insulin hexamer in 1970 to Cryo-EM structures of 
DNA-PK from DNA repair in 2020
Thomas L. Blundell, University of Cambridge

Solving 3D puzzles by integrative modelling using PDB structures
Alexandre M. J. J. Bonvin, Utrecht University

Impact of structural biologists and fifty years of Protein Data Bank operations 
on drug discovery and development
Stephen K. Burley, Rutgers, The State University of New Jersey and University 
of California, San Diego

Cryo-EM of biomolecules at Ångström resolutions
Wah Chiu, Stanford University

50 years of PDB — from crazy idea to treasure
Johann Deisenhofer, University of Texas Southwestern Medical Center

Structural biology of telomerase
Juli Feigon, University of California, Los Angeles

Integrated BioNMR — getting by with a little help from my friends
Angela Gronenborn, University of Pittsburgh

Science, crystallography, reflections: A journey with the PDB over 35 years
Jennifer L. Martin, University of Wollongong

Antibody small molecule conjugates with computationally designed target binding 
synergy
Stephen L. Mayo, California Institute of Technology

Structural insight into SARS-CoV-2 replication and transcription complex (RTC)
Zihe Rao, ShanghaiTech University and Tsinghua University

"Speck"tacular inflammasomes: structures of supramolecular complexes in innate 
immunity
Hao Wu, Harvard Medical School, Boston Children's Hospital



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] Celebrate PDB50 at the Inaugural May 4-5 Event (Early Registration and Poster Abstracts by March 15)

[Christine Zardecki]

Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB 
archive (http://wwpdb.org/pdb50 ).

The inaugural symposium will be held virtually on May 4-5, 2021.  

The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day.  
The event will be recorded and made available to registered participants after 
the meeting.  

Students and postdoctoral fellows are especially encouraged to attend and will 
be eligible for poster awards.

Register at https://www.asbmb.org/meetings-events/pdb50 
 by March 15 for reduced rates.




Speakers

Using HIV-1 reverse transcriptase structures to guide anti-AIDS drug discovery
Edward Arnold, Rutgers, The State University of New Jersey

The evolution of the Protein Data Bank as a community resource
Helen M. Berman, Rutgers, The State University of New Jersey and University of 
Southern California

A personal history of five decades of structural biology and the PDB: From the 
X-ray structure of 2-Zinc insulin hexamer in 1970 to Cryo-EM structures of 
DNA-PK from DNA repair in 2020
Thomas L. Blundell, University of Cambridge

Solving 3D puzzles by integrative modelling using PDB structures
Alexandre M. J. J. Bonvin, Utrecht University

Impact of structural biologists and fifty years of Protein Data Bank operations 
on drug discovery and development
Stephen K. Burley, Rutgers, The State University of New Jersey and University 
of California, San Diego

Cryo-EM of biomolecules at Ångström resolutions
Wah Chiu, Stanford University

50 years of PDB — from crazy idea to treasure
Johann Deisenhofer, University of Texas Southwestern Medical Center

Structural biology of telomerase
Juli Feigon, University of California, Los Angeles

Integrated BioNMR — getting by with a little help from my friends
Angela Gronenborn, University of Pittsburgh

Science, crystallography, reflections: A journey with the PDB over 35 years
Jennifer L. Martin, University of Wollongong

Antibody small molecule conjugates with computationally designed target binding 
synergy
Stephen L. Mayo, California Institute of Technology

Structural insight into SARS-CoV-2 replication and transcription complex (RTC)
Zihe Rao, ShanghaiTech University and Tsinghua University

"Speck"tacular inflammasomes: structures of supramolecular complexes in innate 
immunity
Hao Wu, Harvard Medical School, Boston Children's Hospital


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

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[ccp4bb] User Survey: Tell RCSB PDB About Your Interests

[Christine Zardecki]

RCSB PDB wants to learn more about our user. 

Please take this brief survey  and be 
entered into a drawing for PDB50 Structural Biology Playing Cards: 
https://www.surveymonkey.com/r/65WVGB7
The results of this survey will help us better understand RCSB.org usage and 
user research interests.

All survey responses are greatly appreciated 
.





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[ccp4bb] Obituary for John D. Westbrook

[Christine Zardecki]

John D. Westbrook Jr. (1957-2021), Research Professor at Rutgers University and 
Data & Software Architect Lead for the RCSB PDB, passed away on October 18, 
2021.

He was incredibly beloved and respected by his colleagues at Rutgers and 
throughout the world, known for his dry wit and endless enthusiasm for thinking 
about all aspects of data and data management.

John had a long and highly successful career developing ontologies, tools, and 
infrastructure in data acquisition, validation, standardization, and mining in 
the structural biology and life science domains. His work established the 
PDBx/mmCIF data dictionary and format as the foundation of the modern Protein 
Data Bank (PDB) archive (wwPDB.org).

More than twenty-five years ago, while still a graduate student, John 
recognized the importance of a well-defined data model for ensuring delivery of 
high quality and reliable structural information to data users. He was the 
principal architect of the mmCIF data representation for biological 
macromolecular data. Based on a simple, context-free grammar (without column 
width constraints), data are presented in either key-value or tabular form. All 
relationships between common data items (e.g., atom and residue identifiers) 
are explicitly documented within the PDBx Exchange Dictionary 
(mmcif.wwpdb.org). Use of the PDBx/mmCIF format enables software applications 
to evaluate and validate referential integrity within any PDB entry. A key 
strength of the mmCIF technology is the extensibility afforded by its rich 
collection of software-accessible metadata.

The current PDBx/mmCIF dictionary contains more than 6,200 definitions relating 
to experiments involved in macromolecular structure determination and 
descriptions of the structures themselves. The first implementation of this 
schema was used for the Nucleic Acid Database, a data resource of nucleic 
acid-containing X-ray crystallographic structures. Today, this dictionary 
underpins all data management of the PDB. Since 2014, it has served as the 
Master Format for the PDB archive. It also forms the basis of the Chemical 
Component Dictionary (wwpdb.org/data/ccd), which is used to maintain and 
distribute small molecule chemical reference data in the PDB.

In 2011, the Worldwide Protein Data Bank (wwPDB) PDBx/mmCIF Working Group was 
established to enable direct use of PDBx/mmCIF format files within major 
macromolecular crystallography software tools and to provide recommendations on 
format extensions required for deposition of larger macromolecule structures to 
the PDB. This was a key step in the evolution of the PDB archive, which enabled 
studies of macromolecular machines, such as the ribosome, as single PDB 
structures (instead of split entries with atomic coordinates distributed among 
different entry files). In 2019, mandatory submission of PDBx/mmCIF format 
files for deposition was announced (Adams et al. Acta Crystallographica D75, 
451-454).

To ensure the success of the PDBx/mmCIF dictionary and format, John worked with 
a wide range of community experts to extend the framework to encompass 
descriptions of macromolecular X-ray crystallographic experiments, 3D 
cryo-electron microscopy experiments, NMR spectroscopy experiments, protein and 
nucleic acid structural features, diffraction image data, and protein 
production and crystallization protocols. Most recently, these efforts have 
been focused on developing compatible data representations for X-ray free 
electron (XFEL) methods, and for integrative or hybrid methods (I/HM). I/HM 
structures, currently stored in the prototype PDB-Dev archive 
(pdb-dev.wwpdb.org), presented new challenges for data exchange among rapidly 
evolving and heterogeneous experimental repositories. Proper management of I/HM 
structures in PDB-Dev also required extension of the PDBx/mmCIF data dictionary 
to include coarse-grained or multiscale models, which will be essential for 
studying macromolecular structures in situ using cryo-electron tomography and 
other bioimaging methods.

John contributed broadly to community data standards enabling interoperation 
and data integration within the biology and structural biology domains. His 
efforts have included (i) describing the increasing molecular complexity of 
macromolecular structure data, (ii) representing new experimental 
methodologies, including I/M techniques, and (iii) expanding the biological 
context required to facilitate broader integration with a spectrum of 
biomedical resources. John’s work has been central to connecting 
crystallographic and related structural data for biological macromolecules to 
key resources across scientific disciplines. His efforts have been described in 
more than 120 peer-reviewed publications, one of which has been cited more than 
21,000 times according to the Web of Science (Berman et al. Nucleic Acids 
Research 28, 235-242). Eight of his most influential published papers have 
appeared in the Internation

[ccp4bb] Explore Computed Structure Models Alongside PDB Data at RCSB.org | Register for Virtual Crash Course

[Christine Zardecki]

Explore Computed Structure Models Alongside PDB Data at RCSB.org 
<http://rcsb.org/>

In addition to nearly 200,000 experimentally-determined PDB structures, 
RCSB.org now offers access to ~1 million Computed Structure Models (CSMs) from 
AlphaFoldDB and RoseTTAFold (from Model Archive). Both software tools build on 
decades of methodological research on structure prediction and rely on open 
access to the immense number of sequences in genomic sequence databases and to 
the PDB archive. This release includes the pre-packaged collection of 999,255 
AlphaFold models released on 01-Jun-2022 (based on model organism proteomes; 
global health proteomes; Swiss-Prot sequences; and MANE (Matched Annotation 
from NCBI and EMBL-EBI)) and 1,106 core eukaryotic protein complexes produced 
by RoseTTAFold and AlphaFold2 from the ModelArchive.

Users can query, organize, visualize, analyze, and compare experimental 
structures and CSMs side-by-side.  Visit RCSB.org for details: 
https://go.rutgers.edu/wwor80ww

Want to learn more? Register Now for Virtual Crash Course: Exploring Computed 
Structure Models from Artificial Intelligence/Machine Learning at RCSB.org on 
Thursday September 22, 2022 (1:00 - 3:00 pm EDT).

Registration is required for the Zoom meeting information, but attendance is at 
no charge. Please sign up at https://forms.gle/xbvDdgCoX7NmzK556 
<https://forms.gle/xbvDdgCoX7NmzK556>


------
CHRISTINE ZARDECKI
Deputy Director, RCSB Protein Data Bank
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
E: christine.zarde...@rcsb.org
RCSB.org | facebook <https://www.facebook.com/RCSBPDB> | twitter 
<https://twitter.com/buildmodels>

Coronavirus Resources: RCSB.org/covid19 <https://rcsb.org/covid19>

Job openings for Scientific Software Developers, Postdocs: 
www.rcsb.org/pages/jobs <https://www.rcsb.org/pages/jobs>



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[ccp4bb] RCSB PDB looking for Postdoctoral Fellows to join our multidisciplinary development team at UC San Diego

[Christine Zardecki]

The Challenge: Develop innovative analysis, integration, query, and 
visualization tools for 3D biomolecular structures to help accelerate research 
and training in biology, medicine, and related disciplines. In these projects, 
we employ the latest advances in computer science to develop highly interactive 
features and scalable services and workflows. The overall goal is always to 
develop highly interactive features for the RCSB PDB website.

Two Postdoctoral Fellow positions are available: one focused on Visualization 
(position #1104 ) 
and Machine Learning/Biological Assemblies (position #1105 
). Possible 
project areas include:

Innovative representations for 3D structural data, including biological 
assemblies
Visualizations for comparative analyses
Multiscale rendering for exploring large structures
Using machine learning to build the next generation search engine for molecular 
biology
This is a unique opportunity to engage in leading edge research, development, 
and outreach activities of the RCSB PDB with worldwide impact. 

For more information, contact us at 
http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/job_listings.html


--
Twitter: http://twitter.com/#!/buildmodels
Facebook:  http://www.facebook.com/RCSBPDB

[ccp4bb] Scientific Software Developer position at RCSB Protein Data Bank (RCSB.org) at the University of California San Diego (UCSD)

[Christine Zardecki]

For contact information and other positions, please see 
http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/job_listings.html
 


Scientific Software Developer

Develop, implement, and maintain complex scientific and web-based software 
systems for the RCSB Protein Data Bank (RCSB PDB; http://www.rcsb.org 
) at the University of California San Diego (UCSD).

The Scientific Software Developer will work closely and collaboratively with 
other software developers and scientists at the San Diego Supercomputer Center 
(SDSC) and the RCSB PDB partner sites to expand RCSB.org 's 
functionality and reliability as a premier biological data and information 
resource.

* Develop new scalable algorithms for the mining and analysis of the rapidly 
growing PDB archive using leading edge Big Data technologies. Design and 
implement user interfaces for the query, analysis, reporting, and visualization 
of 3D structural information and associated annotations.
* Integrate external database resources with RCSB PDB to provide a structural 
view of biology. Help lead the design of databases and data warehouses to store 
and aid in the query of data.
* Recommend and implement changes in software development, maintenance and 
system standards for analysis algorithms, tools, and infrastructure.
* Serve as a recognized expert on relevant scientific and technical aspects of 
the various web, web services, and database components of the RCSB PDB. Stays 
abreast of the latest development in structural and computational biology and 
new technologies.
* Applies advanced bioinformatics concepts to design, develop, modify, debug, 
and evaluate highly complex software programs and web tools. Translates 
scientific problems into scalable and maintainable software solutions that meet 
end user needs.

Qualifications: Advanced understanding of programming in one or more languages 
is required (Java, Python or Javascript); In-depth understanding of 
Bioinformatics; understanding of Biology or Chemistry; and an advanced degree

--
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Facebook:  http://www.facebook.com/RCSBPDB

[ccp4bb] Please Respond to the RCSB PDB User Survey and Raffle

[Christine Zardecki]

RCSB PDB is running an online survey to help us better understand 
RCSB.org and PDB-101 users and interests.

People who submit their responses at https://www.surveymonkey.com/r/RLRGRXX
can also enter into a drawing for a poster, 2018 calendar, or Zika model.

All users are encouraged to respond.

Thanks in advance for your consideration!

Christine

--
Twitter: http://twitter.com/#!/buildmodels
Facebook:  http://www.facebook.com/RCSBPDB

[ccp4bb] Applications Open for Director, RCSB Protein Data Bank

[Christine Zardecki]

Rutgers, The State University of New Jersey (New Brunswick, NJ, USA) invites 
applications for a distinguished scientist, focused on 3D structures of 
biological macromolecules, to be appointed with tenure at the level of Full 
Professor (or above). This role will involve directorship of the Research 
Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, 
RCSB.org) and the opportunity to be part of a leadership team building a new 
Rutgers-New Brunswick Chancellor-level institute for artificial intelligence, 
data science, and cyberinfrastructure. The University is seeking an expert in 
computational and/or experimental structural biology with an outstanding record 
of accomplishment and excellent future promise, working at the interface 
between biology/medicine and the computational, statistical, physical, 
chemical, mathematical, or bioengineering sciences.

A detailed description of the position is available 
<https://www.rcsb.org/pages/director-job>: 
https://www.rcsb.org/pages/director-job

--
CHRISTINE ZARDECKI
Deputy Director, RCSB Protein Data Bank
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
E: christine.zarde...@rcsb.org
RCSB.org | facebook <https://www.facebook.com/RCSBPDB> | twitter 
<https://twitter.com/buildmodels>

Coronavirus Resources: RCSB.org/covid19 <https://rcsb.org/covid19>

Undergraduates and Graduates:  Opportunities for Scientific Software-focused 
Summer Research, Gap Year, and Postdoctoral Research: www.rcsb.org/pages/jobs





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[ccp4bb] Register Now for a Virtual Deep Dive into Computed Structure Model Exploration at RCSB.org

[Christine Zardecki]

Join us as we demonstrate how RCSB.org serves as your gateway to structural 
data exploration on Tuesday April 30, 2024 from noon-1pm Eastern, 9-10am Pacific
This event will equip you with the knowledge of how to use RCSB.org features to 
navigate 3D predicted protein structures in the context of 
experimentally-determined PDB structures.

Registration is required for the Zoom meeting information, but attendance is at 
no charge.
Please sign up at https://go.rutgers.edu/1ztidbcw

Contact i...@rcsb.org  with any questions.


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[ccp4bb] Register Now for a May 14 Webinar on Understanding PDB Validation: Which experimental structures should I rely on?

[Christine Zardecki]

Join RCSB PDB for a webinar on Understanding PDB Validation on Tuesday May 14, 
2024 from 11am-12pm Pacific, 2pm-3pm Eastern.

Learn about primary PDB structure quality metrics, including those in the 
validation slider graphic; how PDB structure quality varies across the archive; 
and identify good structure(s) for research from RCSB.org

Who should attend?

Professionals and graduate students interested in learning about strategies to 
take full advantage of PDB data in the fields of:

Structural biology
Cheminformatics and computational chemistry
Bioinformatics and computational biology
Journal article reviewers and editors will also benefit from this webinar.

After the seminar, users will:

Know about the primary PDB structure quality metrics
Understand PDB structure quality varies across the archive 
Know how to identify good structure(s) for research from RCSB.org
Registration is required for the Zoom meeting information, but attendance is at 
no charge.
Please sign up at https://go.rutgers.edu/ikmomgei


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[ccp4bb] Opening: RCSB PDB Director and Tenured Professor of Chemistry and Chemical Biology

[Christine Zardecki]

-field nuclear magnetic resonance, biomedical 
research innovation and mass spectrometry, X-ray, and microscopy core 
facilities. The RCSB PDB Director will leverage collaborative opportunities 
across units and University core facilities at the Institute for Quantitative 
Biomedicine—including cryo-electron microscopy and macromolecular mass 
spectrometry—to drive leadership and innovation in structural biology, making 
breakthrough innovations at the intersection of chemistry, data science, 
biology, and medicine.

Rutgers is a leading national research university and the State of New Jersey’s 
preeminent, comprehensive public institution of higher education, committed to 
building a beloved community through University Equity and Inclusion. 
Established in 1766, the university is the eighth-oldest higher education 
institution in the United States. More than 70,000 students and 23,400 full- 
and part-time faculty and staff learn, work, and serve the public at Rutgers 
locations across New Jersey and around the world. Our community values 
leadership, respect, innovation and creativity, research and scholarship, 
integrity, and teamwork.



--
CHRISTINE ZARDECKI
Associate Director, RCSB Protein Data Bank
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
E: christine.zarde...@rcsb.org
RCSB.org | facebook <https://www.facebook.com/RCSBPDB> | twitter 
<https://twitter.com/buildmodels>

Coronavirus Resources: RCSB.org/covid19 <https://rcsb.org/covid19>

Undergraduates and Graduates:  Opportunities for Scientific Software-focused 
Summer Research, Gap Year, and Postdoctoral Research: www.rcsb.org/pages/jobs





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