wwPDB launched the Deposition Tool for structures determined using X-ray crystallography on January 27, 2014 as part of a new Deposition and Annotation System. Using this system, more than 4,200 structures have been deposited and annotated, and >1,700 structures released in the archive.
Features of the new system include use of the PDBx/mmCIF data format, which produces more uniform data; the ability to replace data files pre- and post-deposition; enhanced communication; improved annotation; and geometric and experimental data checking based on recommendations from expert task forces. Detailed information and video tutorials are available.
As a result of this successful release, ADIT has been retired at RCSB PDB and PDBj for new depositions of structures determined from X-ray crystallographic experiments. Existing, in-progress ADIT sessions of X-ray crystallographic structures can be accessed until July 19, 2015.
ADIT will continue to accept depositions from other experimental methods. Deposition tools for NMR and 3DEM are being developed by the wwPDB.
Questions and comments should be sent to firstname.lastname@example.org.
RCSB PDB Mobile is a universal app that enables the general public, researchers and scholars to search the PDB and visualize protein structures using mobile devices.
Freely available for the iPhone/iPod/iPad and Android (2.3.3 and above), RCSB PDB Mobile can be used to search the entire PDB database, view the latest released structures, access MyPDB accounts, and view the entire catalog of Molecule of the Month articles.
A program update has been released at the Apple Store and Google play which includes the latest Molecule of the Month article and bug fixes for recent indexing issues.
Known issues will be listed on the RCSB PDB Mobile support page. Currently, the molecular viewer used in the app (NDKmol) cannot support large structures with more than 62 chains and/or 99,999 atoms, and cannot be used on Android 5.0 (Lollipop). The app will be updated as new versions are made available.
RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank(2014) Bioinformatics doi:10.1093/bioinformatics/btu596
The Winter 2015 issue of the RCSB PDB Newsletter is now available.
Articles explore 2014 statistics and highlights, large structures in the PDB, 15 years of the Molecule of the Month, and more.
This issue's Education Corner describes how teachers have Mentored High School Students for the RCSB PDB HIV Video Challenge.
RCSB PDB's Newsletter is published and archived online. Sign up to receive electronic updates each quarter.
In January 2000, the Molecule of the Month was launched with a feature on myoglobin, the first structure determined using X-ray crystallography. Since then, 180 Molecule of the Month articles have explored the structure and function of PDB macromolecules from AAA+ proteases to Zinc fingers. These articles are one of the most popular features of the RCSB PDB website and are utilized by classrooms around the world.
Authored and illustrated by David S. Goodsell, Molecule of the Month features have grown over the years to include curated, interactive views, discussion topics, and links to specific examples. The carefully composed illustrations, available free for use as high resolution images, have been reproduced and used in countless educational resources. These unique pictures of molecular machines provided both inspiration and content for the Art of Science traveling exhibit.
Through the years, Molecule of the Month features have become tightly integrated with other RCSB PDB initiatives. Many posters, paper models, and animations have been built using these features. The articles have also led to the creation of the Structural View of Biology browser, which offers top-down contextual exploration of the PDB. January's focus on Cascade and CRISPR will be used in this year's protein modeling event in the Science Olympiad.
To celebrate this special anniversary, we have assembled an online PDF calendar for 2015 that features a small selection of the many molecular highlights of the past 15 years.
In 2014, students created impressive videos illustrating the structural biology of HIV. This year, RCSB PDB is challenging students to tell a story of defeating, combating, and controlling the HIV pandemic at the molecular level using structures from the PDB.
Videos will be judged by considered for three awards: Judge's Choice, Viewer's Choice, and Service to the Community. The deadline for submission is May 31, 2015.
RCSB PDB offers many resources to help students get started. Visit PDB-101 for an overview, rules, HIV-related education materials, tutorials on making videos, and more.
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RCSB PDB newsletters.
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