From the evening of July 8th to the morning of July 11th, NCBI and the RCSB PDB will assist the International Society for Computational Biology (ISCB) in hosting a sequence-structure hackathon focused on integrating protein structure information and viewers with genomic sequence and variants, pharmacogenomic binding, and general laboratory practice. To apply for this hackathon, complete this form (approximately 10 minutes to complete). Applications are due June 10th, 2016 by 5 pm ET.
Working groups of 5-6 individuals will be formed into five or six teams. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. The potential subjects for this iteration are:
Please see the application for specific team projects.
After a brief organizational session, teams will spend three days analyzing a challenging set of scientific problems related to a group of datasets. Participants will analyze and combine datasets in order to work on these problems.
Datasets will come from the public repositories housed at the NCBI, PDB and elsewhere.
All pipelines and other scripts, software and programs generated in this course will be added to a public GitHub repository designed for that purpose. A manuscript outlining the design and usage of the software tools constructed by each team will be submitted to an appropriate journal.
To apply, complete this form (approximately 10 minutes to complete). Applications are due June 1st, 2016 by 5 pm ET. Participants will be selected from a pool of applicants based on the experience and motivation they provide on the form. Prior participants and applicants are especially encouraged to reapply. The first round of accepted applicants will be notified on June 3rd by 5 pm ET, and have until June 6th at noon to confirm their participation.
If you confirm, please make sure it is highly likely you can attend, as confirming and not attending bars other data scientists from attending this event. We understand this hackathon is going on during an information-dense scientific meeting, so we ask that attendees attend at least part of three out of five scientific sessions in the draft daily schedule. Please include a monitored email address, in case there are follow-up questions.
Please contact email@example.com with any questions.
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For the third year, RCSB PDB is inviting high school students to create short videos that tell a molecular story of health and disease. This year's focus is the structural view of sugar metabolism and its complications leading to diabetes. To get started, teams are encouraged to use PDB-101 materials related to diabetes and molecular visualization.
Videos may be submitted from March 8 - May 29, 2016 for review by our esteemed panel of judges. Award winners will be announced on June 14, 2016.
DCC: a Swiss army knife for structure factor analysis and validation H. Yang, E. Peisach, J. D. Westbrook, J. Young, H. M. Berman and S. K. BurleyJ. Appl. Cryst. (2016). 49 doi: 10.1107/S1600576716004428
DCC is a wrapper for third-party software packages to aid in structure factor analysis and validation. As the results are recorded in PDBx/mmCIF format, the output from DCC can be used in automatic data pipelines.
The program can be downloaded from sw-tools.rcsb.org.
A full list of RCSB PDB publications is available.
The new Insulin and Diabetes poster illustrates how structural biology has revealed the details of insulin signaling and how this knowledge is being used to create new and better treatments for diabetes
The poster is built around the watercolor painting Insulin in Action, which includes glucose (small white circles), insulin (yellow), and the insulin receptor (light green), among others.
Explore more resources and articles about insulin and diabetes using the PDB-101 Browser.
NHGRI's National DNA Day commemorates the completion of the Human Genome Project and the discovery of DNA's double helix. It's also a day for students, teachers, and the public to learn more about genetics and genomics.
The Spring 2016 issue of the RCSB PDB Newsletter is now available.
Articles highlight Wellcome Trust Image Awards, visualization of electron density maps for ligands, the 2016 High School Video Challenge, and more.
This issue's Education Corner is related to the Video Challenge. In this interview, Jed Dannenbaum, a USC Professor of the Practice of Cinematic Arts, gives advice on telling scientific stories with videos.
RCSB PDB's Newsletter is published and archived online. Sign up to receive electronic updates each quarter.
Last week, the 3D structure of the Zika virus, determined by cryo-electron microscopy, was released in the PDB archive. Public availability of the Zika virus atomic coordinates to medical researchers worldwide will accelerate new antiviral drug and vaccine development.
PDB ID: 5ire
The 3.8Å Resolution Cryo-EM Structure of Zika Virus Devika Sirohi, Zhenguo Chen, Lei Sun, Thomas Klose, Theodore C. Pierson, Michael G. Rossmann, Richard J. Kuhn Science (2016) doi: 10.1126/science.aaf5316
Build a paper model of the Zika virus based on this entry in this new PDB-101 activity.
Read about RCSB PDB resources and how they can be used in research and education:
RCSB Protein Data Bank: A Resource for Chemical, Biochemical, and Structural Explorations of Large and Small Biomolecules (2016) Christine Zardecki, Shuchismita Dutta, David S. Goodsell, Maria Voigt, and Stephen K. Burley J. Chem. Educ., 2016, 93 (3), pp 569-575 doi: 10.1021/acs.jchemed.5b00404 A full list of RCSB PDB publications is available.
Website/HTTP access to PDB data files is improving as RCSB PDB moves to a scalable, cloud-based service that will better support our growing user community. Access to this service via http://files.rcsb.org is not rate-limited or throttled for heavy users, and programmatic usage is encouraged.
This method is being used to deliver PDB entry data files (PDB and PDBx/mmCIF formats) from the Download Tool and from Structure Summary pages (Display and Download options). Data are returned faster and more reliably.
Simplified URLs point to compressed and uncompressed files to better enable use of PDB data in software applications:
Two RCSB PDB images have been highlighted with 2016 Wellcome Image Awards. David S. Goodsell's painting of Ebola Virus Proteins has been selected as the overall winner, with Maria Voigt's molecular animation of Clathrin also recognized with an award.
Goodsell's painting was created for his RCSB PDB Molecule of the Month article on Ebola Virus Proteins, and also turned into a related video. This intricate painting shows this tiny, notoriously lethal virus in minute detail, using the structural information available in the Protein Data Bank archive.
Voigt's Clathrin illustration is part of RCSB PDB's traveling Art of Science exhibit, which uses the context of a community art gallery to introduce new audiences to to the beauty of structural biology. This exhibit is currently on display at the FlexSchool in Fanwood, NJ.
These are two of the 20 winning images selected as the best in science image making from all those acquired by the Wellcome Images picture library in the past year. The awards were presented at a ceremony at the Science Museum in London on March 15, where the images are now on show to the public. Other award-winning images include pathways of nerve fiber in the brain, delicate golden scales on a Madagascan sunset moth and a digitally reconstructed skeleton showing atheroma, the "furring up" of arteries that supply blood to the brain which can cause stroke.
16 science centers, museums and galleries will be displaying the winning images in their own styles to spark imaginations everywhere. This year the images will also be appearing as far afield as the Africa Centre for Population Health in South Africa, the Polytechnic Museum in Moscow, Russia, and the Massachusetts Institute of Technology.
The images are available to view on the Wellcome Image Awards website along with the stories behind the images and their creators. The images already feature in Wellcome Images collections, where they can be accessed and used along with more than 40,000 other contemporary biomedical and clinical images. The Awards were established in 1997 to reward contributors to the collection for their outstanding work.
View sigma-weighted 2m|Fo|-d|Fc| electron density "mini-maps" for bound ligands using the JSmol 3D View. This feature is available for ligands with more than one atom (ions excluded) in PDB entries with structure factor data. Different sigma values can be selected.
The feature can be accessed from an entry's Structure Summary page in the Small Molecule's section or from the bottom of the 3D View page.
RCSB PDB's Gene View illustrates the correspondences between the human genome and 3D structure. All human genes have been mapped to representative PDB protein chains (chosen from sequence clusters at 40% sequence identity) to show which regions of a gene are available in PDB coordinates.
PDB is now a billion-atom archive. Over a hundred thousand entries--proteins, DNA, RNA, and all the tiny molecules associated with them--capture the nanoscale details of these billion atoms. Use RCSB PDB's to start exploring:
Searches at rcsb.org now return PDB structures using a redesigned layout. The user interface puts the structures at the top of the page. The left column provides summary information at a glance by indicating the distribution of structures in categories, including by organism, UniProt molecule name, taxonomy, and more. A search for collagen, for example, shows that 277 structures related to collagen were determined by X-ray crystallography. The items in this column can also be used to refine a search. In this same example, clicking on X-ray Resolution less than 1.5 Å will display the corresponding high resolution structures.
Similar to RCSB PDB's home page and Structure Summary pages, the responsive layout of the Search Results page is designed to appear well on mobile devices.
Search Results can be used to generate tables, download data, and create galleries of images. For more information, view the What's New page or enter a search term in the top box.
For the third year, RCSB PDB invites all high school students to create short videos that tell a molecular story of health and disease. This year's focus is the structural view of sugar metabolism and its complications leading to diabetes. To get started, teams are encouraged to use PDB-101 materials related to diabetes and molecular visualization.
Videos may be submitted from March 8 - May 29, 2016. Award winners will be announced on June 14, 2016.
For more information, sign up for the Video Challenge Monthly Newsletter or visit the challenge webpage.
Protein modeling is one of several competitive events taking place 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.
In protein modeling, teams of high school students demonstrate their understanding of protein structure and function by building 3D models. The theme of this year's event, designed by MSOE and RCSB PDB, is focused on biosynthesis and subsequent signaling of dopamine and serotonin.
RCSB PDB recently judged ~100 models in regional competitions in New Jersey, and will also participate in the February San Diego Regional event.
Many thanks to the RCSB PDB judges, 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.
The online portal PDB-101 is aimed at teachers, students, and the general public to promote molecular explorations through biology and medicine. This website ("101", as in an entry-level course) presents introductory materials that introduce beginners to the structures of proteins and nucleic acids contained in the PDB archive.
The PDB-101 resource has been reorganized to provide better access to curricular materials, paper models, Molecule of the Month articles, and other materials developed by the RCSB PDB. Users can search the website for related materials using molecule name or keyword. The Browse option can be used to explore available PDB-101 resources organized by topics such as immune system and renewable energy.
The Winter 2016 issue of the RCSB PDB Newsletter is now available.
Articles highlight 2015 statistics, the new wwPDB Deposition Tool, RCSB PDB's 2016 protein-drug calendar, website features for query and analysis, and more.
In this issue's Education Corner, CCDC's Amy Sarjeant describes Using 815,527 Crystal Structures to Teach Chemistry: The Cambridge Structural Database.
RCSB PDB's Newsletter is published and archived online. Sign up to receive electronic updates each quarter.
Since January 2014, the new wwPDB Deposition & Annotation (D&A) system has been used to submit and annotate >12,000 X-ray structure depositions and to release >6,800 entries in the PDB archive.
The wwPDB has now expanded this system to support structures from 3DEM and NMR experiments. The wwPDB D&A system interoperates with EMDB and BMRB to enable joint depositions of both atomic coordinates (PDB) and electron density maps (EMDB) or NMR experimental data (BMRB). Both PDB and EMDB/BMRB accession codes will be issued simultaneously after the entry is deposited.
Visit wwpdb.org for more information on this new D&A system.
A new calendar highlighting protein-drug complexes in the PDB archive is available for download in PDF (4 MB) and PowerPoint (20 MB) formats.
Proteins are tiny molecular machines. While not visible with the naked eye, their structures and functions can be investigated and understood through various experimental methods. Proteins perform many of the tasks needed to support living cells. Illnesses, such as cancer, can occur when they are prevented from performing their normal jobs. Other ailments are caused when foreign proteins (such as from bacteria or viruses) interfere with ours. Most drugs are small chemicals, even smaller than proteins, that work by binding to target proteins and modifying their actions within our cells. Other drugs are modified proteins that can take the place of improperly operating native proteins.
Some of our most powerful anticancer drugs completely disable an essential molecular machine, without which the cell cannot survive. These drugs kill cancer cells outright. Other drugs, such as cholesterol lowering agents, blunt the action of less-critical proteins to benefit patients.
We know a great deal about how drugs work because scientists in academe and the pharmaceutical industry are able to examine drug-protein complexes at the level of individual atoms. These three-dimensional (3D) atomic structures allow us to see how drugs bind to their protein targets in exquisite detail. Frequently, these structures suggest ways to modify the structure of the drug to better fit the target protein, either to improve efficacy or to reduce the likelihood of side effects. These structures of proteins and drugs highlighted in this calendar, along with many others, can be explored using the RCSB PDB.
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