Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

non-PDB format compatible entries

... chain ids with more than 2 characters - complex sheet records(e.g. a large beta barrel structure) - large B factor (≥ 1000) - 5- ... As such, the split entries have now been consolidated into a single entry and the individual split entries have been obsoleted. ...

2021 PDBj web server transition

... the search matches in mmCIF, mmJSON or arbitrary JSON formats - A new PDBj data archive has been prepared (https://data.pdbj.org/), ... where we have re-arranged our data files into a more logical and cleaned-up manner. - The PDBMLplus format has ...

PDBj omni-search functionality

... the associated category (e.g. for "PDB keywords" above, a PDBj Mine keyword search will be performed). Hitting [ENTER] (or ... hits [ENTER]. To indicate that the system has found a perfect match, a carriage return symbol (↵) is prepended to the result. Holding ...

Basic Usage

... on the search button right from the field. 4. You will find a summary page for the entry (such as this: mine:1GOF ). For ... list page for the keyword. Click the PDB ID, you will find a summary page for the entry. [Data Deposition] Please refer to Data ...

Spanner

... optimize the resulting structure. The resulting PDB, as well as a log file, will be emailed to you when the modeling task ... finishes. If an error prevented a homology model from being generated (for example, when the alignment ...

PDBj Mine search results

... results are split up over several pages, each page holding a specific amount of search results (see here about customizing this ... you can also download the results in tsv and json format. A wide range of result fields are available: - PDB ID - Structure ...

Download PDBETA

... . You (each licensee is addressed as "you") are granted a non-exclusive license to use the Software on the following terms ... limited to, the implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the quality and ...

Functional annotation example

... geometry of surface-exposed residues enabled the identification of a putative active site near theHPDDGEloop located near the N- ... several eukaryotes), 1uan was proposed to be a hydrolase acting on a disaccharide substrate. Since the 1uan structure was ...

[wwPDB] Access Depositions Using ORCiD

... entries’ deposition interfaces without the need to login again using a deposition ID or password.

[wwPDB] wwPDB to switch to version 3 of the EMDB data model

... model is version 1.9.6, while version 3, which facilitates a richer representation of the metadata about EMDB entries, was introduced in ... Archive, an XML file named emd-xxxxx.xml, will become a v3 XML file that follows the structure of the latest version ...

Derived databases

... pdbj.org/eF-seek/top.do ProMode Elastic ProMode Elasticis a database of normal mode analysis of PDB data. The ... URL: https://pdbj.org/promode-elastic/ hGTOP hGTOP is a database containing annotations of proteins in human, mouse and rat ...

[wwPDB] PDB Turns 49

... The Foundation raised funds to help support PDB40, a symposium celebrating the 40th anniversary of the archive; workshops ... ; and educational publications. The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, ...

[wwPDB] Announcing the New PDBx/mmCIF User Guide

... mmCIF ecosystem We are excited to announce the launch of a detailed PDBx/mmCIF File Format User Guide. As the ... and examples of essential PDBx/mmCIF records, aimed to facilitate a smooth transition to this format for depositors and users alike. ...

[wwPDB] CASP15 Call for Targets

... particularly by the AlphaFold and more recently RosettaFold. As a result of these advances, computed protein structures are becoming ... much more widely used in a broadening range of applications. Since CASP14, the protein ...

[wwPDB] 50 Years of the PDB

... The Foundation raised funds to help support PDB40, a symposium celebrating the 40th anniversary of the archive; workshops ... ; and educational publications. The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, ...

News on 2007-12-12

... structures) and restraints (for NMR structures) will be a mandatory requirement for PDB deposition. These data must be deposited ... paper is published (HPUB). This policy was developed as a result of comments and recommendations from the PDB user community, ...

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

... shifts and restraints have been deposited to the PDB - A valid topology file or specific comments must be present to ... during structure calculation. The NMR restraints validation software employs a more general approach recommended by NMR-VTF, independently ...

News on 2010-05-06

... please contact us or info@wwpdb.org. References 1. JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, ... Laue (2005). The CCPN data model for NMR spectroscopy: development of a software pipeline . Proteins 59, 687-696. 3. JF Doreleijers, ...

[wwPDB] Modifications to support for SHEET and ligand SITE records in June 2021

... cases where the definition of the strands within a beta sheet cannot be presented in a linear description. For example, in PDB ... within the beta sheet forming the barrel are instances of a single beta strand making contacts on one side with multiple other ...

Mine 2 RDB local install

... PDBj. The dump files have been designed to be used with a recent version of PostgreSQL. In the future we will also release ... the mine2 database in the same manner. Weekly update We've developed a new system for upgrading local Mine 2 RDB data, which is ...

eF-site

... coloring attributes of the molecular surface in the form of a set of polygons. Electrostatic potentials and hydrophobic properties are ... discribed together by the surface color in such a way that red to blue colors correspond negative to ...

[wwPDB] wwPDB Events at IUCr

... Brinda Vallat (RCSB PDB) will speak about PDB-Dev: A prototype system for archiving integrative structures - Saturday August 26: ... PDB) will present RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific ...

Customizing the PDBj web interface

... expand panels using the main menu as an example. Please take a look at the following video which illustrates this effect. To make ... the panel. An afterimage version of the panel will be shown as a preview as you move the panel along the y-axis. Once ...

We will exhibit at \

... to realize “science harmonized with society” and a “society harmonized with science” through dialogue and collaboration while ... 2. "Feeling" by touching the molecule models made with a 3D printer 3. "Constructing" by making molecules with paper ...

[wwPDB] Coming July 29: Improved Carbohydrate Data at the PDB

... this page after data release. The wwPDB has created a new ‘branched’ entity representation for polysaccharides, describing ... in the Chemical Component Dictionary (CCD) and applied a branched entity representation to oligosaccharides for >8000 PDB entries ...

222624

PDB entries from 2024-07-17

PDB statisticsPDBj update infoContact PDBjnumon