Year 2015 News Articles

Exploring Structure Quality

24-Feb-2015

Structure Summary pages for X-ray crystal structures provide access to validation information based upon the recommendations of the wwPDB X-ray Validation Task Force:

  • A PDF report containing Ramachandran plots created using MolProbity. Ramachandran plots provide an independent method to evaluate the conformational quality of protein structures, and offer a visual representation of any outliers tabulated in the Validation Report PDF. For more information about MolProbity, see Chen et al. (2010) Acta Cryst D66:12-21.
  • The "slider" graphic displayed on the page gives an indication of the quality of the determined structure as compared with previously deposited PDB entries using several important global quality indicators
  • The full PDB Validation Report PDF, which contains the slider graphic and other information to provide an assessment of the quality of a structure and highlight specific concerns (visit the wwPDB for more information)

Previously, Ramachandran plots were located on the Structure Summary Geometry tab, which has been retired. Additional validation data and statistics are available from the Structure Summary Links tab, including reports by WHAT_CHECK and PROCHECK.



Ramachandran plots for entry for 1CBS

Ramachandran plots for entry 1cbs as created by MolProbity.



2015 High School Video Challenge Materials

17-Feb-2015



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.

Many resources are offered to help students get started, including the new video Learn about HIV from the RCSB PDB. Visit PDB-101 for an overview, rules, HIV-related education materials, tutorials on making videos, and more.



BioJava 4.0.0 Released

10-Feb-2015

BioJava is an open source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and support manipulation of sequences and 3D structures.

Through BioJava, RCSB PDB releases algorithms and file parsers used at rcsb.org, including algorithms used in the protein Comparison Tool, some of the tracks of the Protein Feature View, and the algorithm for detecting symmetry in biological assemblies.

BioJava also contains a reference implementation for parsing and processing PDBx/mmCIF format data files.

A BioJava tutorial is available to help  facilitate rapid application development for bioinformatics.

BioJava: an open-source framework for bioinformatics in 2012.
Bioinformatics (2012) 28: 2693-2695.



NJ Science Olympiad Protein Modeling Results

03-Feb-2015

55 teams from high schools across New Jersey demonstrated their understanding of 3D protein structure at three regional Science Olympiad competitions held in January.

Students use Jmol to build a model on the day of the event.

Students use Jmol to build a model on the day of the event.

The models built by students are examples of proteins involved in genome editing. This year's event was designed by MSOE and RCSB PDB, and highlights related Molecule of the Month columns as a resource. Protein modeling will be one of several events at Science Olympiad tournaments across the country and in the National events in May. Teams are recognized for their performance in individual events and in the overall tournament.

The top scoring teams in the New Jersey Science Olympiad regional protein modeling events were

Northern (NJIT, Jan 15, 2015)

  1. Al-Ghazaly HS
  2. Montville Township HS
  3. Biotechnology HS
  4. Morris Hills HS
  5. Parsippany Hills HS
  6. Millburn HS

Central (UCC, Jan 7, 2015)

  1. West Windsor-Plainsboro HS North - II
  2. South Brunswick HS - II
  3. South Brunswick HS - I
  4. Randolph HS - I
  5. Union County Vocational Technical Schools - I
  6. JP Stevens HS - I

Southern (CCC, Jan 15, 2015)

  1. Montgomery HS - II
  2. Princeton HS - I
  3. Montgomery HS - I
  4. New Providence HS - II
  5. Princeton HS - II
  6. Lawrence HS
Science Olympiad at UCSD campus

RCSB PDB will also participate in the San Diego Regional event on February 21, and recently hosted a protein modeling workshop at UCSD.

Science Olympiad Judges

Judges Luigi Di Costanzo, Shuchismita Dutta (also an event creator), and Yuhe Liang

Many thanks to the RCSB PDB judges in NJ (Luigi Di Costanzo, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, Brian Hudson, Yuhe Liang, Ezra Peisach, Chenghua Shao, Lihua Tan, Christine Zardecki, and Marina Zhuravleva), the NJ Science Olympiad organizers and volunteers, and the host colleges (Camden County, Union County, and NJIT).

We look forward to seeing the teams at the NJ state finals in March! Related materials for protein modeling preparation are hosted by MSOE and RCSB PDB.



wwPDB Deposition Tool Replaces ADIT for Crystal Structures

27-Jan-2015

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 info@wwpdb.org.



RCSB PDB Mobile for iOS and Android Update

20-Jan-2015

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





Winter Newsletter Published

13-Jan-2015

Winter 2015 Newsletter Published

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.



New Calendar Celebrates 15th Anniversary of Molecule of the Month

06-Jan-2015

15th Anniversary of Molecule of the Month

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.



Video Challenge for High School Students

06-Jan-2015

15th Anniversary of Molecule of the Month

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.