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 ...

228 new PDB entries have been released on 2024-09-18. 225158 entries are now available in total. Please refer to PDB / EMDB latest information for other updates.

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 ...

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 ...

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 ...

Structures determined by integrative and hybrid structure determination methods (IHM) are now available alongside experimental structures in the PDB archive. These structures are deposited into and processed by the PDB-Dev system. Each IHM structure is ...

Introduction The atomic coordinate data in PDB is "asymmetric unit", which includes minimum essential. It doesn't always mean actual functional unit in organisms. The functional structures are called "biological unit", some of them are equal to the ...

Advisors from the Scientific Community - Koga, Nobuyasu (Institute for Protein Research, The University of Osaka) - Mitsuoka, Kaoru (Research Center for Ultra-High Voltage Electron Microscopy, The University of Osaka) - Senda, Toshiya (Institute of ...

Congratulations to biocurator Dr. Irina Persikova on processing over 10,000 PDB depositions. She is the seventh biocurator in the wwPDB reached this milestone. Irina has received Ph.D. training in Solid State Physics and provided over 20 years of ...

We already finished providing PDBMLplus files written in the XML format. Instead, please use PDBj Mine RDB search or the mmjson-plus files written in json format. Introduction Before we provided PDBMLplus as the merged data of PDBML, XML-formatted PDB ...

URL: http://rdf.wwpdb.org/pdb PDB/RDF is a collection of PDB data in the Resource Description Framework (RDF) format. The RDF format is the standard format for the Semantic Web. An ontology defined in the Web Ontology Language (OWL) is also provided for ...

Benefits of the PDBx/mmCIF ecosystem We are excited to announce the launch of a detailed PDBx/mmCIF File Format User Guide. As the foundation for depositing, annotating, and archiving structural data across diverse experimental techniques, the ...

Congratulations to RCSB PDB's Yuhe Liang on processing over 10,000 PDB depositions. He is the sixth biocurator to reach this milestone in the wwPDB. Dr. Liang received his PhD in biophysics from Peking University, China with expertise in macromolecular ...

Please cite PDBj or PDBj services with the following references listed below. Please also refer to Terms and Conditions on using contents in PDBj site. Also see "Cite a PDB structure entry" to cite an individual PDB entry. - Cite PDBj - Cite a PDBj ...

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 - 日本語 (A3 6 pages A4 12 pages) 2021 Calendar for celebrating 50th anniversary of PDB ...

This page provides some examples of SQL queries that can be executed from the PDBj Mine interface at https://pdbj.org/rdb/search. You can use these samples at SQL Search of PDBj Mine or PDBj Mine:REST API. Documentation describing the SQL schema can be ...

PDBj Mine is a web interface to search the PDB. PDBj Mine has the following basic features: 1. PDBj Mine is based on a relational database. 2. Allows enhanced keyword search. 3. Detailed queries can be performed using using SQL. - PDBj Mine:SQL ...

The standardization of protein modification handling ensures that there is a single correct approach to handling each protein modification that occurs within the PDB archive. However, there are many existing PDB entries that contain protein modifications ...

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, ...

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

- 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. ...

- Head Kurisu, Genji, Ph.D. (Prof., IPR, Osaka Univ.) - Kurisu, Genji, Ph.D. (Prof., IPR, Osaka Univ.) - Group for Data-in of PDB/EMDB Nakagawa, Atsushi, Ph.D. (Prof., IPR, Osaka Univ.) Yu, Jian, Ph.D. (Assoc. Prof., IPR, Osaka Univ.) Cho, Hasumi (Chen, ...

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 ...

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

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 ...