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231 new PDB entries have been released on 2024-04-10.

231 new PDB entries have been released on 2024-04-10. 218196 entries are now available in total. Please refer to PDB / EMDB latest information for other updates.

[wwPDB] CASP16 Call for Targets

CASP (Critical Assessment of protein Structure Prediction) is in search for targets. CASP (Critical Assessment of protein Structure Prediction) experiments are held every two years. Recent rounds have seen dramatic increases in modeling accuracy, ...

Announcement of the PDBj Newsletter Vol.24 release

Now, we have released the PDBj Newsletter Vol.24.

Newsletter

- Vol.24 (March 2024) English (pdf 2.9M) / Japanese (pdf 2.9M) - Vol.23 (March 2023) English (pdf 2.7M) / Japanese (pdf 3.0M) - Vol.22 No.2 (March 2022) English (pdf 2.4M) / Japanese (pdf 2.6M) - Vol.22 (December 2021) English (pdf 2.6M) / Japanese (pdf 3. ...

Newsletter / Public Relations Resources

Newsletter Latest (Vol.24, 6 pages) - 日本語 English Previous news letters are here. Flyer for researchers (2 pages) - 日本語 English Leaflet for general people (6 pages) - 日本語 2021 Calendar for celebrating 50th anniversary of PDB - - English ...

[wwPDB] Paper Published on NMR Restraint Validation

We are pleased to announce the publication of this manuscript, addressing the challenge of validation of experimental biomolecular NMR structures against restraint data. The NMR exchange (NEF) and NMR-STAR formats provide a standardized approach for ...

[wwPDB] Paper Published on CryoEM Archiving and Validation Recommendations

A workshop was held at EMBL-EBI (Hinxton, UK) in January 2020 to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis and setting community recommendations. The outcomes of this meeting have ...

[wwPDB] Poster Prize Awarded at The Biophysical Society Meeting

The wwPDB Foundation made an award for outstanding student presentations at the 2024 Biophysical Society Meeting (February 10-14, Philadelphia, PA). Irin Pottanani Tom Mechanisms of Light Signalling and Allosteric Regulation in Dual Sensor ...

Notice of Service Suspension (ASH, DASH, SeSAW, MAFFTash, Spanner, SFAS)

Due to a lack of IT personnel, the following services are now suspended. - ASH - DASH - SeSAW - MAFFTash - Spanner - SFAS

ASH

Dear ASH User, As of February 2024, the laboratory of Genome Informatics, headed by Daron Standley, has suspended the operation of the ASH web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data ...

SeSAW

Dear SeSAW User, As of February 2024, the laboratory of Genome Informatics, headed by Daron Standley, has suspended the operation of the SeSAW web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data ...

Spanner

Dear Spanner User, As of February 2024, the laboratory of Genome Informatics, headed by Daron Standley, has suspended the operation of the Spanner web service. The main reason for the suspension is a lack of IT personnel needed to perform security and ...

MAFFTash

Dear MAFFTash User, As of February 2024, the laboratory of Genome Informatics, headed by Daron Standley, has suspended the operation of the MAFFTash web service. The main reason for the suspension is a lack of IT personnel needed to perform security ...

SFAS

Dear SFAS User, As of February 2024, the laboratory of Genome Informatics, headed by Daron Standley, has suspended the operation of the SFAS web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data ...

DASH

Dear DASH User, As of February 2024, the laboratory of Genome Informatics, headed by Daron Standley, has suspended the operation of the DASH web service. The main reason for the suspension is a lack of IT personnel needed to perform security and data ...

[wwPDB] Biocurator Milestone: >10,000 Depositions Processed

Congratulations to biocurator Minyu Chen on processing over 10,000 PDB depositions. She is the second biocurator to reach this milestone in the PDBj and the fifth in the wwPDB. Yumiko Kengaku reached this milestone in April 2021. Minyu received her PhD ...

[wwPDB] Preprint Published on NMR Restraint Validation

Graphical Abstract This manuscript addresses this challenge of validation of experimental biomolecular NMR structures against restraint data. The NMR exchange (NEF) and NMR-STAR formats provide a standardized approach for representing commonly used NMR ...

[wwPDB] Preprint Published on CryoEM Archiving and Validation Recommendations

The number of released EMDB entries per year in a number of resolution bins, from 2010 until December 2023 A workshop was held at EMBL-EBI (Hinxton, UK) in January 2020 to discuss data requirements for deposition and validation of cryoEM structures, ...

[wwPDB] Preprint Published on NextGen Archive

A new paper describes how the recently-announced NextGen Archive provides centralized access to integrated annotations and enriched structural information for PDB data: NextGen Archive: Centralising Access to Integrated Annotations and Enriched ...

[wwPDB] Prizes Awarded at The Biophysical Society Japan Meeting

The wwPDB Foundation made awards to outstanding student presentations at the 2023 The Biophysical Society Japan Meeting (November 14-16, Nagoya, Japan). Keisuke Kasahara Thermodynamic analysis of Fv-supercharged antibody–antigen interactions and ...

[wwPDB] Resources for Supporting the Extended PDB ID Format (pdb_00001abc)

wwPDB anticipates that all the four character PDB accession codes (PDB ID) will be consumed by 2029. With the continuous growth of PDB archive, wwPDB has revised the PDB accession code format by extending its length and prepending “PDB” (e.g., "1abc" ...

[wwPDB] Time-stamped Copies of PDB and EMDB Archives

New archive snapshots are available. A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org, https://s3.rcsb.org) as of January 2, 2024 has been added to ftp://snapshots.wwpdb.org, https://s3snapshots.rcsb.org (AWS), and ftp://snapshots.pdbj.org. ...

[wwPDB] Improved Depositor Experience Using ORCiD

ORCiD login button at in OneDep circled in red Since March 2023, depositors can use their ORCiDs to access the OneDep system. This authentication method enables contact authors to access sessions without sharing passwords. Using ORCiD with OneDep ...

[wwPDB] PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats

The PDB three-character Chemical Component IDs are consumed and PDB has begun issuing five-character alphanumeric accession codes for CCD IDs in the OneDep system. To avoid confusion with current four-character PDB IDs, four-character codes are not used. ...

[wwPDB] Deprecation of FTP File Download Protocol in the PDB Archive

The FTP protocol for file downloads has been losing popularity over the years in favor of HTTP/S. There are many advantages of HTTP/S including speed, statelessness, security (HTTPS), and better support. Importantly during the past 2-3 years the main web ...

218196

PDB entries from 2024-04-10

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