Guide to Understanding PDB Data: Small Molecules
The constantly-growing PDB is a reflection of the research that is happening in laboratories across the world. This can make it both exciting and challenging to use the database in research and education.
PDB-101's Guide to Understanding PDB Data was created to help users navigate through the contents of the archive without having a detailed background in structural biology.
Topics cover biological assemblies, molecular graphics programs, R-value and R-free, and more.
A new chapter has been added to help users examine the Small Molecule Ligands are represented in the PDB archive. Topics in this article include:
- General Overview
- Representation of Ligands in Entry Files
- Free Ligands vs. Ligands in Polymers
- Biologically Interesting Molecules
- Electron Density Visualization
- Ideal and Model Ligand Representations
Award-Winning Structural Biology/Diabetes Videos
For the fourth year, RCSB PDB invited high school students to tell molecular stories in video. This year's challenge focused on the molecular view of the diabetes treatment and management. The challenge entries (all available online) demonstrate a wide variety of topics with many creative story-telling approaches.
Our panel of expert judges scored the videos based on scientific content (40%), creativity (20%), overall impact (20%), entertainment value (10%), and production quality (10%). In addition, the general public voted for the Viewer's Choice Award.
Congratulations to the 2017 Winners (which can be viewed online):
- First Place: Insulin: From Bacteria To You By Andrew Ma, George Song, and Anirudh Srikanth of West Windsor-Plainsboro High School South in Princeton Junction, NJ (Team Advisor: Matthew Foret)
- Second Place: Metformin and DPP 4 Inhibitors Take the DIE out of Type 2 Diabetes By Julie Chaimowitz, Fiona Lu, Lori Mohs, and Amy Ni of East Brunswick High School, East Brunswick, NJ (Team Advisor: Louise Jasko)
- Third Place: Sugary Solutions: An In Depth Look at the Treatment of Type 2 Diabetes By Audrey Guo and Anna Shi of West Windsor-Plainsboro High School South, Princeton Junction, NJ (Team Advisor: Meenakshi Bhattacharya)
- Viewer's Choice: Type 2 Diabetes: Meet It Beat It By Kerwin Chen, Raisa Khuda, and Tasnuba Sukanna of Stuyvesant High School in New York, NY (Team Advisor: Gilbert Papagayo)
Many thanks to the expert judges, students, teachers, parents, judges, and voters who made this exciting competition happen!
Vote Now for the Video Viewer's Choice Award
RCSB PDB recently challenged high school students to create videos telling the story of diabetes treatment and management. Watch the challenge entries online and cast your vote now for your favorite video.
Voting for the Viewers Choice Award is now open until June 6th 12:59 EST. Winners will be announced at PDB-101 and rcsb.org on June 13, 2017.
Learning Structural Biology in Virtual Reality
The latest Education Corner describes Learning in Virtual Reality: Revolutionizing education with Autodesk's Molecule Viewer. This viewer is a free, online 3D visualization tool for modern scientists and learners to explore, share, and present molecular data. It was recently used to curate an present a structural biology symposium on the retinal protein world.
Published quarterly in our Newsletter, each Education Corner offers an account of how members of the community use the PDB to educate students. If you would like to submit an Education Corner column, please send an email to firstname.lastname@example.org.
The spring RCSB PDB Newsletter also includes the report of the Global Life Sciences Data Resources (GLSDR) Working Group, plans for updating all PDBx/mmCIF model files to the V5 version of the PDBx/mmCIF dictionary, and open Postdoctoral Fellow positions at RCSB PDB at UCSD. Recent PDB-101 highlights are presented, including a 2017 NSF/Popular Science Vizzie Award, 2016 FASEB BioArt Award, and recognition by Genetic Engineering & Biotechnology News as Best of the Web.
Spring Newsletter Published
Topics include the report of the Global Life Sciences Data Resources (GLSDR) Working Group, plans for updating all PDBx/mmCIF model files to the V5 version of the PDBx/mmCIF dictionary, and open Postdoctoral Fellow positions at RCSB PDB at UCSD. Recent PDB-101 highlights are presented, including a 2017 NSF/Popular Science Vizzie Award, 2016 FASEB BioArt Award, and recognition by Genetic Engineering & Biotechnology News as "Best of the Web."
Zika Illustration Named People’s Choice
Since 2003, the Vizzies Challenge has recognized visualizations of scientific data that are “exemplars of information made beautiful.”
At the 2017 Vizzies, David Goodsell's painting for the Molecule of the Month was recognized by the National Science Foundation (NSF) and Popular Science as one of the best science images of the year and selected as the “People’s Choice” in the category of illustration.
See the Art of Science at Rutgers' S.T.E.A.M. Women's Empowerment Conference on March 25
RCSB PDB’s traveling art exhibit The Art of Science will be featured at the Dr. Jewel Plummer Cobb S.T.E.A.M. Women’s Empowerment Conference entitled Nevertheless, She Persisted on March 25th at the Rutgers Busch Student Center in Piscataway. This event is hosted by the Division of Student Affairs and #stemHERstoryRU.
Dr. Jewel Plummer Cobb was an influential educator, trailblazer and scientist who served as the sixth Dean of Douglass at Rutgers from 1976 to 1981. Dr. Cobb passed away on New Year’s Day, 2017, at the age of 92, in Maplewood, NJ.
S.T.E.A.M. Women’s Empowerment Conference is a forum where individuals will be inspired to take personal responsibility in owning and embracing their story and identity. Admission is free; registration is online.
PDB-101 is "Best of the Web"
PDB-101 is an online portal developed by RCSB PDB for teachers, students, and the general public to promote exploration in the world of proteins and nucleic acids. PDB-101 features support learning about the diverse shapes and functions of these biological macromolecules and their relationship to biomedicine and agriculture, from protein synthesis to health and disease to biological energy.
These resources are made freely available thanks to support from the National Science Foundation (DBI-1338415), the National Institutes of Health, and the US Department of Energy.
Enter the 2017 Video Challenge
For the fourth year, RCSB PDB invites high school students across the USA to create short videos that tell a molecular story of health and disease. This year’s focus is the Molecular View of Diabetes Treatment and Management. To get started, teams are encouraged to use PDB-101 resources related to diabetes, diabetes treatments, and molecular visualization.
Videos may be submitted from March 7, 2017– May 22, 2017. Award winners will be announced on June 13, 2017.
For more information, sign up for the Video Challenge Monthly Newsletter and visit the challenge webpage at PDB-101.
Molecular Origami: Build 3D models of Zika virus
Zika virus infects people around the globe. For most, the virus causes a mild illness that is quickly fought off by the immune system. But a connection between Zika infection in pregnant women and birth defects has underscored the need to find ways to fight the disease. Zika is spread by mosquitos, so our primary defense is to remove breeding sites and to take measures to avoid being bitten. There are a few examples of the Zika virus and related structures available in the PDB archive. Public availability of these atomic coordinates to medical researchers worldwide will accelerate new antiviral drug and vaccine development.
Winter Newsletter Published
Read about 2016 milestones and a review of recently-added website tools and features.
In the Education Corner, Rebecca Alford and Jeffrey Gray (Johns Hopkins) describe the Rosetta Commons summer Research Experience for Undergraduates (REU). Interested in applying? Submissions are due February 1, 2017.
2016 FASEB BioArt Winner
Video stills of three HIV enzymes are among the 2016 Winners of FASEB's BioArt Competition. This year’s 10 winning images and three videos represent a wide range of research in the biomedical and life sciences, from technology that may aid in recovery from spinal cord injury to a portrait of the New York City skyline “printed” in yeast.
Winning entries were unveiled on FASEB’s website and will be exhibited at the National Institutes of Health.