News 2021
Structural Science: New Ways to Teach the Next Generation
11/30/2021
Watch Presentations from the October 6 PDB50 Celebration
11/23/2021
Congratulations Mickayla!
11/15/2021
New Flyer: SARS-CoV-2 Genome and Proteins
11/09/2021
PDB50 Recognized in the Congressional Record
11/02/2021
Undergrads/Grads: Apply to the Molecule of the Month Boot Camp (January 2022)
11/01/2021
Celebrating PDB and Rutgers Structural Biologists
10/28/2021
Obituary for John Westbrook
10/27/2021
PDB50: The Game
10/26/2021
Making Big Data Biology
10/24/2021
Supporting the PDB Archive
10/22/2021
50 Years of Community Building
10/21/2021
Rutgers Today
10/20/2021
PDB Turns 50
10/19/2021
Take the RCSB.org User Survey and Win
10/19/2021
Structural Biology Playing Cards
10/19/2021
New PDB Citation MeSH Network Explorer
10/18/2021
Happy Birthday, Irving Geis
10/18/2021
Celebrating PDB50 in Virtual Reality
10/15/2021
The PDB in JBC
10/14/2021
Synergies between the PDB and the community
10/13/2021
Biocurator Milestone: >10,000 Depositions Processed
10/12/2021
Video: Celebrating PDB50
10/11/2021
PDB Pioneers
10/08/2021
User Survey: Tell RCSB PDB About Your Interests
10/07/2021
PDB and the Pandemic
10/06/2021
Structural Biology and Nobel Prizes
10/05/2021
The Nobel Prize in Physiology or Medicine 2021
10/04/2021
Fall Newsletter Published
10/03/2021
Video: Opioids and Pain Signaling
09/28/2021
Register for an October 6 PDB50 Celebration
09/21/2021
Congratulations, Amy and Mickayla!
09/13/2021
Bringing Molecular Structure to Life
09/09/2021
Poster Prize Awarded at ISMB/ECCB
08/31/2021
Poster Prize Awarded at ACA
08/24/2021
PDB50 at ACS August 25
08/17/2021
Impact of PDB Structures on Anti-Cancer Drug Approvals
08/10/2021
VAX Paintings
08/03/2021
PDB50: Function Follows Form
07/26/2021
Summer Newsletter Published
07/15/2021
Molecular Landscapes
07/06/2021
PDB50 at ACS August 25
06/22/2021
Guide to Understanding PDB Data: Carbohydrates
06/15/2021
Congratulations to Poster Prize Winners
06/08/2021
Education Corner: Exploring the Structure-Function Relationship
06/01/2021
How the Protein Data Bank Changed Biology
05/25/2021
Evolution of PDB-101
05/21/2021
Award-Winning Videos on Molecular Mechanisms of Drugs for Mental Disorders
05/18/2021
CellPAINT Contest Winners
05/12/2021
Vote Now for the Viewer's Choice Award
05/07/2021
Explore the History of the PDB
04/27/2021
Annual Report Published
04/24/2021
EXTENDED: Enter the 2021 CellPAINT Contest by May 6
04/24/2021
Celebrate DNA Day on April 25
04/23/2021
Register for PDB50 by May 1
04/18/2021
Scientific Software Developers and Postdocs
04/15/2021
Spring Newsletter Published
04/13/2021
Developers: HTTPS enforcement starts May 10
04/09/2021
Download Molecular Landscapes
04/06/2021
Enter the 2021 CellPAINT Contest by May 1
04/01/2021
Molecular Landscapes: E. coli
03/23/2021
Submit Abstracts for PDB50
03/07/2021
More than 1,000 SARS-CoV-2 Coronavirus Protein Structures Available
03/02/2021
High School Students: Submit Videos By April 27
02/25/2021
Join Us at the Feb 24 Biophysical Society Job Fair
02/21/2021
PDB50: Submit Posters by March 15
02/15/2021
Molecular Valentines
02/11/2021
PDB50 Backgrounds For Virtual Meetings
02/02/2021
Powerful New Tools for Exploring 3D Structures
01/26/2021
Winter Newsletter Published
01/11/2021

Structural Science: New Ways to Teach the Next Generation

11/30/2021

The 70th Annual Meeting of the American Crystallographic Association was held from August 2-7, 2020, virtually. An issue of Structural Dynamics contains articles submitted by authors participating in the annual transactions symposium which focused on new ways to teach the next generation of structural scientists.

Articles include:

  • Teaching a large-scale crystallography school with Zoom Webinar (Joseph D. Ferrara, Amanda Cochran, Mark Del Campo, Christian R. Göb, Pierre Le Maguerès, Mathias Meyer, Horst Puschmann, Christian Schürmann, Alexandra Stanley, Paul N. Swepston, Akhilesh Tripathi, Fraser White and Jakub Wojciechowski)
  • Molecular storytelling for online structural biology outreach and education (David S. Goodsell, Shuchismita Dutta, Maria Voigt and Christine Zardecki)
  • A science education model for large collaborative centers (William J. Bauer and Sarah B. Woodruff)
  • Inviting others to life in reciprocal space (Cora Lind)
  • X-ray Lite: A 1-credit pass/fail crystallography course (Carla Slebodnick)
  • Developing a macromolecular crystallography driven CURE (Krystle J. McLaughlin)
  • Transactions from the 70th Annual Meeting of the American Crystallographic Association: Structural Science—New Ways to Teach the Next Generation (Joseph Tanski, Christine Zardecki, Andrey Yakovenko and Cassandra Eagle)


Watch Presentations from the October 6 PDB50 Celebration

11/23/2021

The Biophysical Society hosted a virtual symposium on October 6, 2021, highlighting some of the high-impact applications of protein structural data, with a particular focus on the areas of structure prediction and membrane protein biophysics.

The recorded presentations from that day are available from the BPS Video Library

Session I. Enabling Understanding of Protein Structure, Function, and Design

  • Helen M. Berman, Rutgers - The State University of New Jersey and RCSB PDB
  • John Jumper, DeepMind, Inc, United Kingdom
  • Ruth Nussinov, NIH, USA and Tel Aviv University, Israel
  • Christine Orengo, University College London, United Kingdom
  • David Baker, University of Washington, USA

Session II. Molecular Biophysics of Membrane Proteins

  • Stephen K. Burley, Rutgers - The State University of New Jersey and RCSB PDB
  • Jue Chen, Rockefeller University and HHMI, USA
  • Nieng Yan, Princeton University, USA
  • Linda Columbus, University of Virginia, USA
  • Rod MacKinnon, Rockefeller University and HHMI, USA

Organizers

  • Helen M. Berman, Rutgers - The State University of New Jersey and RCSB PDB, USA
  • Stephen K. Burley, Rutgers - The State University of New Jersey and RCSB PDB, USA
  • Gaetano T. Montelione, Rensselaer Polytechnic Institute, USA


Congratulations Mickayla!

11/15/2021

Mickayla Bacorn (University of Maryland, Baltimore County)Mickayla Bacorn (University of Maryland, Baltimore County)

This past summer, four students joined members of the RCSB PDB and the Khare Lab at Rutgers to study protease evolution across all Coronaviridae using bioinformatics tools.

2021 RCSB PDB Summer Scholars: Clockwise, starting with upper left: Mary Agnes Balogun (Morgan State), Mickayla Bacorn (University of Maryland, Baltimore County), Cassandra Olivas (California State University Stanislaus), and Amy Wu Wu (University of Puerto Rico-Mayaguez)2021 RCSB PDB Summer Scholars: Clockwise, starting with upper left: Mary Agnes Balogun (Morgan State), Mickayla Bacorn (University of Maryland, Baltimore County), Cassandra Olivas (California State University Stanislaus), and Amy Wu Wu (University of Puerto Rico-Mayaguez)

These students were part of RISE at Rutgers, a nationally acclaimed summer research program for outstanding undergraduates from diverse backgrounds. Scholars participate in cutting-edge research in the biological, physical, and social/ behavioral sciences, math, engineering, and exciting interdisciplinary areas under the guidance of carefully matched faculty mentors.

Mickayla Bacorn's poster Biochemical analysis and review of the active site evolution of SARS-CoV-2 and other coronaviruses was recognized with a poster prize at ABRCMS. MaryAgnes Balogun also presented her research on Understanding the active site of the SARS-CoV-2 papain-like proteinase (PLPro) at the meeting.

In August, Mickayla and Amy Wu Wu were each recognized with a Pauling Poster Prize at the 2021 American Crystallographic Association virtual meeting. .


New Flyer: SARS-CoV-2 Genome and Proteins

11/09/2021


PDB50 Recognized in the Congressional Record

11/02/2021

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Congressman Frank Pallone, Jr., who represents New Jersey's 6th district that includes Rutgers University, noted the 50th anniversary of the PDB in the Congressional Record (HTML | PDF)

IN RECOGNITION OF THE 50TH ANNIVERSARY OF THE PROTEIN DATA BANK IN THE UNITED STATES

HON. FRANK PALLONE, JR.

of new jersey

in the house of representatives

Monday, July 19, 2021

Mr. PALLONE. Madam Speaker, I rise today in recognition of the 50th anniversary of the Protein Data Bank (PDB) in the United States and its outsized impact on the scientific community. Established at Brookhaven National Laboratory in 1971, the PDB was created because researchers were unable to share the valuable information they collected due to the lack of advanced computer systems at that time. The PDB solved this problem by serving as a depository for three-dimensional structures of large, biological molecules--such as proteins, DNA, and RNA--and offered the data free of charge or restrictions on usage to individual researchers across the world. Since 1998, I am proud to say the PDB has been co-managed by Rutgers, The State University of New Jersey. Today, the PDB archive in America hosts more than 180,000 structures of molecules found in all living organisms on the planet and is part of a worldwide network with other data centers in Europe and Asia.

The PDB's legacy as the first open-access digital data resource in biology and medicine has led to countless breakthroughs and has democratized access to data in a way that has tremendously benefited the public. Each year, millions of researchers, scientists, educators, students, medical professionals, patients, patient advocates as well as pharmaceutical and biotechnology companies around the world utilize the PDB for basic and applied research, STEM education, and the discovery of lifesaving medicines, particularly anti-viral and anti-cancer drugs. Examples of its profound impact include the more than two million structure data file downloads it generates per day; its contribution to over one million published research papers; and its enabling of research in many subject areas, ranging from Agriculture to Zoology.

But this ambitious project would not have been possible without significant federal investment in scientific research. The National Science Foundation, the Department of Energy, and the National Institutes of Health all contribute funding to the PDB, which generates a return on investment 1,500 times more than federal dollars it receives. This kind of investment clearly demonstrates the importance of the government-university research partnership and why it is critical that we maintain and strengthen that partnership to bolster American innovation and competitiveness for years to come.

In conclusion, Madam Speaker, I offer my congratulations to the PDB in the United States as it celebrates its first 50 years as a leading global resource for experimental data central to scientific discovery, and I look forward to its contributions to science and our society over the next 50 years.


Undergrads/Grads: Apply to the Molecule of the Month Boot Camp (January 2022)

11/01/2021

Science Communication in Biology and Medicine Virtual Boot Camp: January 10–14, 2022Science Communication in Biology and Medicine Virtual Boot Camp: January 10–14, 2022

RCSB PDB and the Rutgers Institute for Quantitative Biomedicine will host a virtual boot camp with a focus on Science Communication in Biology and Medicine. Students will develop writing and 3D molecular visualization skills by collaborating on articles that will be published in the Molecule of the Month series at PDB-101.

The boot camp will run from 9:30am - 4:30pm ET during January 10–14, 2022.

Undergraduates and and graduate students interested in science writing/visualization/communications for biology and medicine should apply to 2022WinterBootCamp@RCSB.org by November 25 with

  • a brief statement of interest (100 words)
  • resume
  • an unofficial transcript
  • science writing sample (from coursework or a published paper that exemplifies your work)

This boot camp is a 1-credit pass/fail course at Rutgers University. A limited number of scholarships for visiting scholars are available.

Visit the Institute for Quantitative Biomedicine for additional details.


Celebrating PDB and Rutgers Structural Biologists

10/28/2021

Celebrating PDB Contributions from Rutgers University Structural BiologistsCelebrating PDB Contributions from Rutgers University Structural Biologists

Tuesday, November 2 2021 | 1:00pm - 6:00pm ET

Register for this virtual event at go.rutgers.edu/khhhy45r

Download Program

  • Protein Data Bank at 50 years of age; Stephen K. Burley, Director, RCSB PDB; IQB; SAS-C&CB; CINJ
  • Solving protein structures with proton detected solid-state NMR: 15 years of progress; Andrew Nieuwkoop, SAS-C&CB
  • Structural elucidation of beta-(1,3)-glucan synthase from Candida glabrata using cryo-electron tomography; Wei Dai, IQB; SAS-CBN
  • Use of structural information to guide successful design of HIV/AIDS treatments; Eddy Arnold, CABM; SAS-C&CB; CINJ
  • How Colicin E1 stoppers the multidrug efflux pump TolC; Jason Kaelber, IQB; Rutgers Cryo-EM and Nanoimaging Facility; CINJ
  • Bacterial response regulators: Diverse regulatory mechanisms enabled by structurally conserved domains; Ann Stock, CABM; RWJMS-B&MB; CINJ
  • Structural biology of transcription and transcriptional regulation; Richard Ebright, WI; SAS-C&CB
  • Investigating alpha-Synuclein amyloid seeding processes by NMR; Jean Baum, SAS-C&CB
  • A story from under the poisonous umbrella: Towards cryo-EM structure determination of the ribosome-Shiga toxin complex; Arek Kulczyk, IQB; SEBS-M&B; CINJ
  • Conformational plasticity in molecular recognition; Guy Montelione, Renssalaer Polytechnic Institute-C&CB (previously Rutgers CABM; SAS-MBB)
  • Structure determination of small proteins by single-particle cryo-electron microscopy; Vasileios Petrou, CII; RNJMS-MB&MG
  • Receptor binding and entry of Hepatitis C Virus; Joe Marcotrigiano, National Institute of Allergy and Infectious Disease (previously Rutgers CABM; SAS-C&CB)
  • Nucleic acid structures and the Protein Data Bank; Helen M. Berman, Ph.D.: Director Emerita, RCSB PDB; IQB; SAS-C&CB

QUESTIONS? Contact Michelle Sanghera msanghera@iqb.rutgers.edu


Obituary for John Westbrook

10/27/2021

John Westbrook at the 2017 Congress and General Assembly of the International Union of Crystallography in Hyderabad, IndiaJohn Westbrook at the 2017 Congress and General Assembly of the International Union of Crystallography in Hyderabad, India

John D. Westbrook Jr. (1957-2021), Research Professor at Rutgers University and Data & Software Architect Lead for the RCSB PDB, passed away on October 18, 2021.

He was incredibly beloved and respected by his colleagues at Rutgers and throughout the world, known for his dry wit and endless enthusiasm for thinking about all aspects of data and data management.

John had a long and highly successful career developing ontologies, tools, and infrastructure in data acquisition, validation, standardization, and mining in the structural biology and life science domains. His work established the PDBx/mmCIF data dictionary and format as the foundation of the modern Protein Data Bank (PDB) archive (wwPDB.org).

More than twenty-five years ago, while still a graduate student, John recognized the importance of a well-defined data model for ensuring delivery of high quality and reliable structural information to data users. He was the principal architect of the mmCIF data representation for biological macromolecular data. Based on a simple, context-free grammar (without column width constraints), data are presented in either key-value or tabular form. All relationships between common data items (e.g., atom and residue identifiers) are explicitly documented within the PDBx Exchange Dictionary (mmcif.wwpdb.org). Use of the PDBx/mmCIF format enables software applications to evaluate and validate referential integrity within any PDB entry. A key strength of the mmCIF technology is the extensibility afforded by its rich collection of software-accessible metadata.

The current PDBx/mmCIF dictionary contains more than 6,200 definitions relating to experiments involved in macromolecular structure determination and descriptions of the structures themselves. The first implementation of this schema was used for the Nucleic Acid Database, a data resource of nucleic acid-containing X-ray crystallographic structures. Today, this dictionary underpins all data management of the PDB. Since 2014, it has served as the Master Format for the PDB archive. It also forms the basis of the Chemical Component Dictionary (wwpdb.org/data/ccd), which is used to maintain and distribute small molecule chemical reference data in the PDB.

In 2011, the Worldwide Protein Data Bank (wwPDB) PDBx/mmCIF Working Group was established to enable direct use of PDBx/mmCIF format files within major macromolecular crystallography software tools and to provide recommendations on format extensions required for deposition of larger macromolecule structures to the PDB. This was a key step in the evolution of the PDB archive, which enabled studies of macromolecular machines, such as the ribosome, as single PDB structures (instead of split entries with atomic coordinates distributed among different entry files). In 2019, mandatory submission of PDBx/mmCIF format files for deposition was announced (Adams et al. Acta Crystallographica D75, 451-454).

To ensure the success of the PDBx/mmCIF dictionary and format, John worked with a wide range of community experts to extend the framework to encompass descriptions of macromolecular X-ray crystallographic experiments, 3D cryo-electron microscopy experiments, NMR spectroscopy experiments, protein and nucleic acid structural features, diffraction image data, and protein production and crystallization protocols. Most recently, these efforts have been focused on developing compatible data representations for X-ray free electron (XFEL) methods, and for integrative or hybrid methods (I/HM). I/HM structures, currently stored in the prototype PDB-Dev archive (pdb-dev.wwpdb.org), presented new challenges for data exchange among rapidly evolving and heterogeneous experimental repositories. Proper management of I/HM structures in PDB-Dev also required extension of the PDBx/mmCIF data dictionary to include coarse-grained or multiscale models, which will be essential for studying macromolecular structures in situ using cryo-electron tomography and other bioimaging methods.

John contributed broadly to community data standards enabling interoperation and data integration within the biology and structural biology domains. His efforts have included (i) describing the increasing molecular complexity of macromolecular structure data, (ii) representing new experimental methodologies, including I/HM techniques, and (iii) expanding the biological context required to facilitate broader integration with a spectrum of biomedical resources. John’s work has been central to connecting crystallographic and related structural data for biological macromolecules to key resources across scientific disciplines. His efforts have been described in more than 120 peer-reviewed publications, one of which has been cited more than 21,000 times according to the Web of Science (Berman et al. Nucleic Acids Research 28, 235-242). Eight of his most influential published papers have appeared in the International Tables of Crystallography.

John has also done yeoman service to the crystallographic community over many years and was recognized with the inaugural Biocuration Career Award from the International Society for Biocuration in 2016.

For the International Union of Crystallography, John served on the Commission for Maintenance of CIF Standard (COMCIFS), the Working Group on Data Diffraction Deposition (DDDWG), and the Committee on Data (CommDat). He also served as an Associate Editor for Acta Crystallographica Section F.

John was a long-standing member of the American Crystallographic Association, and served on the Data, Standards & Computing Committee. He also served on the Metadata Interest Group for the Research Data Alliance.

John is survived by his wife, Bonnie J. Wagner-Westbrook, Ed.D. and his devoted Mother-in-Law, Joan N. Wagner of Clinton Twp., NJ; many cousins including Chandler Turner (of Portsmouth, VA), Ann (Turner) Heyes (of Tasmania, Australia) and Louise (Turner) Brown (of Oakland CA).

Visitation will take place on Saturday, November 6, 2021 from 2-4pm with Memorial Service at 4pm. All at Scarponi-Bright Funeral Home, 26 Main Street, Lebanon, NJ. Interment will be private.

Memorials can be made to Capicats or an organization of choice in his honor.

Additional information is available at Scarponi-Bright.

John D. Westbrook Jr (1957–2021) Acta Cryst (2021) D77: 1475-1476 doi: 10.1107/S2059798321011402


PDB50: The Game

10/26/2021

This game celebrates the 50th anniversary of the PDB by giving players the opportunity to explore the process of structure discovery.

Build your research team and use the tools of structural biology to make ground-breaking discoveries. Prepare samples and grow crystals. Use X-ray crystallography, electron microscopy, and NMR spectroscopy to collect the data necessary to complete a project and deposit a structure to the PDB. Then, move on to the next project...but keep an eye on the competition and try not to get scooped!

Players can download a PDF that contains all the parts of the game or play online with friends at Tabletopia.


Making Big Data Biology

10/24/2021

In 1971, the structural biology community established the single worldwide archive for macromolecular structure data–the Protein Data Bank (PDB). From its inception, the PDB has embraced a culture of open access, leading to its widespread use by the research community. PDB data are used by hundreds of data resources and millions of users.

PDB celebrations throughout 2021 have provided opportunities to reflect on the beginnings of the PDB and how the continued growth of the archive has contributed to knowledge of 3D structure, function, and evolution of biological macromolecules, expanding the frontiers of fundamental biology, biomedicine, and biotechnology.

The story of the beginning of the PDB and other resources is outlined in the book Collecting Experiments a history of the development of biological data collections.

Collecting Experiments: Making Big Data Biology traces the development and use of data collections, especially in the experimental life sciences, from the early twentieth century to the present. It shows that the current revolution is best understood as the coming together of two older ways of knowing—collecting and experimenting, the museum and the laboratory. Ultimately, Bruno J. Strasser argues that by serving as knowledge repositories, as well as indispensable tools for producing new knowledge, these databases function as digital museums for the twenty-first century.

For a review, see Curry, H.A. (2020), Collecting experiments: Making big data biology Strasser, Bruno J. Chicago, IL: University of Chicago Press, 2019 . The FASEB Journal 34: 3445-3447. doi: 10.1096/fj.202000193


Supporting the PDB Archive

10/22/2021

Members of the PDB, past and present, in attendance at the <a href="https://www.wwpdb.org/about/outreach-content/pdb40">PDB40 celebration.</a>
Photo by Constance Brukin.Members of the PDB, past and present, in attendance at the PDB40 celebration. Photo by Constance Brukin.

The PDB has been supported by dedicated team members since it was established in 1971 at Brookhaven National Laboratory (History).

In 2003, the Worldwide Protein Data Bank (wwPDB) was formed to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community. Today, RCSB PDB, PDBe, and PDBj act as deposition, data processing and distribution centers for PDB data.

RCSB PDB team members, located at Rutgers, UCSD/SDSC, and UCSF, support PDB Users by focusing on

  • Deposition/Biocuration: All data deposited undergo expert review. Each structure is examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources, and validated for scientific/technical accuracy.
  • Archive Management/Access: Maintaining the PDB archive includes data dictionary development and standardization and integrating PDB data with other available information.
  • Data Exploration: Support PDB Data Consumers through our open-access web portal RCSB.org that provides tools for structure visualization and analysis.
  • Outreach/Education: Developing resources for teachers, students, and the general public delivered via our PDB-101 website (“101", as in an entry-level course).

Positions are available at RCSB PDB (Rutgers and UCSD) for Scientific Software Developers and Postdocs interested in participating in exciting projects with significant impact on the scientific community.

RCSB PDB team in January 2020 at Rutgers, The State University of New Jersey.RCSB PDB team in January 2020 at Rutgers, The State University of New Jersey.


50 Years of Community Building

10/21/2021

The PDB community of users includes biologists (in fields such as structural biology, biochemistry, genetics, pharmacology); other scientists (in fields such as bioinformatics, software developers for data analysis and visualization); students and educators (all levels); media writers, illustrators, textbook authors; and the general public.

RCSB PDB thanks all of our users for helping build and support the PDB archive.

Meet some of these community members in 50 Years of Community Building at RCSB.org.


Rutgers Today

10/20/2021


PDB Turns 50

10/19/2021

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The PDB was announced on October 20, 1971 in Crystallography: Protein Data Bank Nature New Biology 233: 223 (1971) doi: 10.1038/newbio233223b0.

Today, the PDB archive contains >180,000 structures of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. It is managed by the Worldwide PDB (wwPDB) organization that ensures that the PDB is freely and publicly available to the global community.

The wwPDB has been celebrating this golden anniversary with symposia and events throughout 2021.

Consider supporting 50 years of PDB's spirit of openness, cooperation, and education with a donation to the wwPDB Foundation. The wwPDB Foundation was established in 2010 to raise funds in support of the outreach activities of the wwPDB. The Foundation raised funds to help support PDB50 events, workshops, and educational publications.

The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, charitable, and educational purposes.


Take the RCSB.org User Survey and Win

10/19/2021

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RCSB PDB wants to learn more about our users worldwide. Please take this brief survey and be entered into a drawing for PDB50 Structural Biology Playing Cards.

The results of this survey will help us better understand RCSB.org usage and user research interests.

All survey responses are greatly appreciated!


Structural Biology Playing Cards

10/19/2021

These cards celebrate the 50 year anniversary of the PDB archive, and the structural biologists who have determined and deposited their many biomolecular structures. The traditional suits have been enhanced with structural themes: Infrastructure for clubs, Information for hearts, Catalysis for diamonds, and Energy for spades. The face cards follow a career in science, with training in the clubs, research and breakthroughs in the hearts and diamonds (with a few notable people as the queen and kings of hearts), and professorships with the queen and king of spades.

This set was designed by David S. Goodsell.

The cards can be downloaded from PDB-101

Want a printed set? <a href="https://www.surveymonkey.com/r/65WVGB7">Take this brief survey</a> and be entered into a drawing for PDB50 Structural Biology Playing Cards.Want a printed set? Take this brief survey and be entered into a drawing for PDB50 Structural Biology Playing Cards.


New PDB Citation MeSH Network Explorer

10/18/2021

Find connections between articles describing PDB structures with the new PDB Citation MeSH Network ExplorerFind connections between articles describing PDB structures with the new PDB Citation MeSH Network Explorer

In January, the PDB contained more than 170,000 structures; ~150,000 had corresponding “primary citations” describing these entries in a peer-reviewed journal.

The National Library of Medicine assigns MeSH (Medical Subject Headings) from a controlled vocabulary to index articles for PubMed. MeSH terms typically appear in a hierarchical tree structure that starts with 16 main branches.

The PDB Citation MeSH Network Explorer flattens these trees into co-occurence networks of MeSH terms associated with PDB entries. Each node on the graph is a publication, and nodes are linked when they share MeSH terms.

Publications that share similar MeSH terms are clustered together into Groups; the largest groups are color-coded. Depending on the size of the network, groups contain at least one, two, or three common MeSH terms. Clicking on a node reveals information about the publication, clustered group, and related PDB structures. Nodes that have multiple terms in common are located near each other; nodes that have less in common are located further apart.

This new way of visualizing MeSH terms can provide insights into relationships between PDB primary citations.

This MeSH Explorer has been developed for RCSB PDB by Digital Science and is powered by Dimensions, the world’s largest linked research information dataset.


Happy Birthday, Irving Geis

10/18/2021

RCSB PDB News ImageMyoglobin Fold (1987). Used with permission from the Howard Hughes Medical Institute (www.hhmi.org). All rights reserved.
RCSB PDB News ImagePhoto by Sandy Geis

Irving Geis (October 18, 1908-July 22, 1997) was a gifted artist who helped illuminate the field of structural biology with his iconic images of DNA, hemoglobin, and other important macromolecules. To celebrate Irving Geis' birthday, we invite you to tour the Geis Digital Archive.

Through a collaboration with the Howard Hughes Medical Institute (HHMI), which owns the Geis Archives, RCSB PDB has established a digital archive of Geis' molecular art. This resource displays many of Geis' illustrations in the context of the corresponding PDB structures and related molecular information. These images are also made available for download for noncommercial usage.

Under the direction of RCSB PDB team members, the Geis Digital Archive is being developed by undergraduates. Students created modern visualizations of the molecules featured in Geis' work, and researched the structures to provide background and supporting information about the illustrations. Alex Alvarado (University of Southern California) and Nicole Werpachowski (Fordham College at Lincoln Center) created the initial design of the resource as part of their Rutgers RiSE (Research in Science and Engineering) experience. Their work was funded during the summer of 2015 by an NSF REU. Rutgers students Belle Lin (2015-2016) and Christopher Markosian (2015-2016) continued work on the project. In 2016, Raheel Ahmad (Rutgers), Pamela Amechi (University of Maryland Baltimore Country), and Keyerra Daniels (Winthrop University) expanded the archive as part of the Rutgers RiSE program.

Thanks to the Howard Hughes Medical Institute for their work on this project. Questions about the HHMI Geis Archives should be sent to archives@hhmi.org.

RCSB PDB News ImageImage of Lysozyme by Irving Geis. Used with permission from the Howard Hughes Medical Institute (www.hhmi.org). All rights reserved.
RCSB PDB News ImageImage of PDB ID 1LYZ can be launched in 3D using Jmol.
RCSB PDB News ImageAlex Alvarado, Sandy Geis (Irving's daughter), and Nicole Werpachowski
RCSB PDB News ImageBelle Lin and Christopher Markosian
RCSB PDB News ImageKeyerra Daniels, Raheel Ahmad, and Pamela Amechi


Celebrating PDB50 in Virtual Reality

10/15/2021

Using Nanome software, people can meet in virtual reality (VR) and explore molecular data loaded from the PDB.

To celebrate PDB50, RCSB PDB Biocurator Gregg Crichlow joined Nanome's Carla Gauss inside VR to explore some of the groundbreaking structures in the PDB archive for the field of structure-based drug design: hemoglobin (2DHB), aspirin bound to cyclooxygenase (1PTH), antibiotic-binding proteins (1CEF, 1BLC), and cancer-related proteins (1FPU, 6OIM).

Previously, Gregg explored spike proteins with Nanome; Nanome was also highlighted in an Education Corner feature on Exploring the Molecules of Biological Warfare in Virtual Reality.


The PDB in JBC

10/14/2021

Today, most scientific journals require authors to deposit structural data in the PDB, but that was not always the case. The Journal of Biological Chemistry (JBC) was a pioneer in promoting open access; editors encouraged authors to deposit their structures as early as 1977 and made deposition a requirement for publication in 1989.

As the PDB celebrates its 50th anniversary, JBC has published more structures than any other journal. Highlighting its synergy with the PDB, JBC assembled a collection of JBC Reviews celebrating the scientific areas that have been profoundly touched by the creation of the PDB, and a virtual issue collecting JBC articles that describe a few classic structures and most highly cited papers. These JBC reviews were assembled by Lila Gierasch (JBC) and Helen Berman (Guest Editor).

Explore the milestone PDB structures published in the Journal of Biological Chemistry at RCSB.org.


Synergies between the PDB and the community

10/13/2021

Berman, H.M. Synergies between the Protein Data Bank and the community. Nat Struct Mol Biol 28, 400–401 (2021). doi: <a href="https://doi.org/10.1038/s41594-021-00586-6">10.1038/s41594-021-00586-6</a>Berman, H.M. Synergies between the Protein Data Bank and the community. Nat Struct Mol Biol 28, 400–401 (2021). doi: 10.1038/s41594-021-00586-6

Helen M. Berman was a co-founder of the Protein Data Bank archive that was launched in 1971 and has been committed to the continued development and maintenance of this community resource. She currently serves as Director Emerita of the RCSB PDB, is Distinguished Professor Emerita of Chemistry and Chemical Biology at Rutgers, The State University of New Jersey, and an Adjunct Professor of Biological Sciences at the University of Southern California.

In honor of the 50th anniversary of the PDB, Nature Methods and Nature Structural & Molecular Biology created a special PDB-focused collection.

This collection features a retrospective article by Berman that provides an overview of 50 years of community.

For more on Helen Berman and the PDB, see her memoir as hosted by the American Crystallographic Association and an oral history hosted by the American Institute of Physics.


Biocurator Milestone: >10,000 Depositions Processed

10/12/2021

Congratulations to biocurators Dr. Sutapa Ghosh and Dr. Monica Sekharan on processing over 10,000 PDB depositions. They are the second and third biocurators to reach this milestone. Yumiko Kengaku reached this milestone in April 2021.

Dr. Ghosh received her PhD in structural biology from the University of Calcutta and joined PDB after working in industry in structure-based drug design. Dr. Sekharan received her PhD in Biological Chemistry from the University of Washington with expertise in NMR spectroscopy. During their 15 year career at the PDB, many depositors trusted their professional skills in accurate and comprehensive data analysis and representation. Their deep scientific knowledge, profound data curation expertise and commitment to excellence contributed to the high quality data archive for the benefit of the scientific community. We congratulate Drs. Ghosh and Sekharan with this exciting accomplishment and look forward to their future successes.

RCSB PDB Biocurators Dr. Sutapa Ghosh and Dr. Monica SekharanRCSB PDB Biocurators Dr. Sutapa Ghosh and Dr. Monica Sekharan


Video: Celebrating PDB50

10/11/2021

Video: Celebrating 50 Years of the Protein Data Bank ArchiveVideo: Celebrating 50 Years of the Protein Data Bank Archive

In 1971, the structural biology community established the single worldwide archive for macromolecular structure data–the Protein Data Bank (PDB). From its inception, the PDB has embraced a culture of open access, leading to its widespread use by the research community. PDB data are used by hundreds of data resources and millions of users exploring fundamental biology, energy, and biomedicine.

This video looks at the history and the milestones that shaped the PDB into the leading resource for research and education it is today.

To learn more about PDB50, visit rcsb.org/pdb50.


PDB Pioneers

10/08/2021

In 1971, the structural biology community established the single worldwide archive for macromolecular structure data–the Protein Data Bank (PDB). From its inception, the PDB has embraced a culture of open access, leading to its widespread use by the research community. PDB data are used by hundreds of data resources and millions of users exploring fundamental biology, energy, and biomedicine.

In 2021, RCSB PDB and the wwPDB are celebrating the 50th Anniversary of the PDB with symposia, materials, and more.

Structural biology was born in 1958 with John Kendrew's atomic structure of myoglobin, and in the following decade, the field grew rapidly. By the early 1970's, there were a dozen atomic structures of proteins, and researchers were discovering that they had a goldmine of information. However, the coordinate files for these structures are quite large, and in the days before the internet, it was difficult for individual researchers to share these large files with the growing number of interested structural biologists around the world. The Protein Data Bank archive was created to solve this problem. Depositors would send their coordinates to the PDB, who would then mail them to interested users.

To celebrate the anniversary of the PDB, explore the historic protein structures that inspired the creation of the archive at Molecule of the Month.

PDB Pioneer StructuresPDB Pioneer Structures


User Survey: Tell RCSB PDB About Your Interests

10/07/2021

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RCSB PDB wants to learn more about our users worldwide. Please take this brief survey and be entered into a drawing for PDB50 Structural Biology Playing Cards.

The results of this survey will help us better understand RCSB.org usage and user research interests.

All survey responses are greatly appreciated!


PDB and the Pandemic

10/06/2021

With this week's update, 1,536 SARS-CoV-2-related structures are now freely available from the Protein Data Bank. 55 new SARS-CoV-2 structures were released this week, including Delta and other variants. Access them all, along with related resources, at RCSB.org/covid19.

The first SARS-CoV-2 structure, a high-resolution crystal structure of the coronavirus main protease (PDB 6lu7), was released early in the pandemic on February 5, 2020.

Since then, structural biologists have visualized most of the SARS-CoV-2 proteome, including the spike protein binding to its ACE2 receptor and neutralizing antibodies, and the main protease, the papain-like proteinase, and other promising drug discovery targets. All structures and related data are available for exploration from wwPDB partner websites: RCSB PDB, PDBe, PDBj, and BMRB.

Rapid public release of SARS-CoV-2 structure data has greatly increased our understanding of Covid-19, allowed direct visualization of emerging variants of the virus, and facilitated structure-guided drug discovery and reuse to combat infection. Open access to PDB structures has already enabled design of effective vaccines against SARS-CoV-2.

The response of the research community to the pandemic has highlighted the importance of open access to scientific data in real time. The wwPDB strives to ensure that 3D biological structure data remain freely accessible for all, while maintaining as comprehensive and accurate an archive as possible.

The impact of these 1,536 structures, with more to come stands, as a testament to the importance of open access to structural biology research data.

Download the flyer <a href="https://cdn.rcsb.org/rcsb-pdb/v2/about-us/covid-pitch-flyer-small.pdf">PDB and the Pandemic</A> for an overview of RCSB PDB activities related to coronavirus.Download the flyer PDB and the Pandemic for an overview of RCSB PDB activities related to coronavirus.
Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: <a href="http://pdb101.rcsb.org/sci-art/goodsell-gallery/respiratory-droplet">10.2210/rcsb_pdb/goodsell-gallery-024</a>. <BR><a href="http://pdb101.rcsb.org/browse/coronavirus">Visit PDB-101 for related educational materials.</a>Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-024.
Visit PDB-101 for related educational materials.


Structural Biology and Nobel Prizes

10/05/2021

Nobel Prizes highlighting achievements in physics, chemistry, physiology or medicine, literature and for peace are being announced this week.

Since its inception, many awards have recognized achievements made in molecular biology, structural biology, and related research.

Browse PDB-101 to explore articles and resources that highlight many of the PDB structures and related experimental techniques associated with Nobel Prizes, including a timeline of awards made in Chemistry, Physiology or Medicine, and Physics and corresponding Molecule of the Month articles.


The Nobel Prize in Physiology or Medicine 2021

10/04/2021

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The 2021 Nobel Prize in Physiology or Medicine has been awarded jointly to David Julius and Ardem Patapoutian for their discoveries of receptors for temperature and touch.

PDB structures help us understand these discoveries. Visit PDB-101 to learn more about Piezo1 Mechanosensitive Channel and Capsaicin Receptor TRPV1.

Browse PDB-101 to explore articles and resources that highlight many of the PDB structures and related experimental techniques associated with Nobel Prizes, including a timeline of awards made in Chemistry, Physiology or Medicine, and Physics and corresponding Molecule of the Month articles.


Fall Newsletter Published

10/03/2021

The Fall 2021 issue of the RCSB PDB Newsletter is now online.

This issue highlights PDB50 anniversary celebrations; the New Opioids and Pain Signaling Video; Explore Ligand Quality; User Survey; and more.

Published quarterly, each <a href="http://pdb101.rcsb.org/learn/education-corner">Education Corner</a> describes of how community members use the PDB and related resources.  Contact <a href="mailto:info@rcsb.org">info@rcsb.org</a> to contribute.Published quarterly, each Education Corner describes of how community members use the PDB and related resources. Contact info@rcsb.org to contribute.

Samuel A. McKie (Chapel Prints Co) gives an overview of available SARS-CoV-2 models, and presents new models available for 3D printing and origami paper folding.

Sign up to receive electronic updates each quarter.


Video: Opioids and Pain Signaling

09/28/2021

Pain is one of the most trying experiences of life. On the cellular level it is communicated via special neuronal pathways. On the molecular level, however, pain is communicated like any other sensation, via a set of electrical and chemical signals facilitated by complex molecular machinery. These signals can be modulated by opioids, causing us to feel less pain, or no pain at all. Learn how opioids activate the G-proteins which in turn interact with other proteins to edit the pain signal.Pain is one of the most trying experiences of life. On the cellular level it is communicated via special neuronal pathways. On the molecular level, however, pain is communicated like any other sensation, via a set of electrical and chemical signals facilitated by complex molecular machinery. These signals can be modulated by opioids, causing us to feel less pain, or no pain at all. Learn how opioids activate the G-proteins which in turn interact with other proteins to edit the pain signal.

Video stills and truncated video highlights are available.


Register for an October 6 PDB50 Celebration

09/21/2021

The Biophysical Society will host a virtual symposium on October 6, 2021, highlighting some of the high-impact applications of protein structural data, with a particular focus on the areas of structure prediction and membrane protein biophysics.

Registration is free, however space is limited. Registration deadline is October 4.

Session I. Enabling Understanding of Protein Structure, Function, and Design

  • Helen M. Berman, Rutgers - The State University of New Jersey and RCSB PDB
  • John Jumper, DeepMind, Inc, United Kingdom
  • Ruth Nussinov, NIH, USA and Tel Aviv University, Israel
  • Christine Orengo, University College London, United Kingdom
  • David Baker, University of Washington, USA

Session II. Molecular Biophysics of Membrane Proteins

  • Stephen K. Burley, Rutgers - The State University of New Jersey and RCSB PDB
  • Jue Chen, Rockefeller University and HHMI, USA
  • Nieng Yan, Princeton University, USA
  • Linda Columbus, University of Virginia, USA
  • Rod MacKinnon, Rockefeller University and HHMI, USA

Organizers

  • Helen M. Berman, Rutgers - The State University of New Jersey and RCSB PDB, USA
  • Stephen K. Burley, Rutgers - The State University of New Jersey and RCSB PDB, USA
  • Gaetano T. Montelione, Rensselaer Polytechnic Institute, USA


Congratulations, Amy and Mickayla!

09/13/2021

Amy Wu Wu (University of Puerto Rico-Mayaguez) and Mickayla Bacorn (University of Maryland, Baltimore County)Amy Wu Wu (University of Puerto Rico-Mayaguez) and Mickayla Bacorn (University of Maryland, Baltimore County)

This past summer, four students joined members of the RCSB PDB and the Khare Lab at Rutgers to study protease evolution across all Coronaviridae using bioinformatics tools.

2021 RCSB PDB Summer Scholars: Clockwise, starting with upper left: Mary Agnes Balogun (Morgan State), Mickayla Bacorn (University of Maryland, Baltimore County), Cassandra Olivas (California State University Stanislaus), and Amy Wu Wu (University of Puerto Rico-Mayaguez)2021 RCSB PDB Summer Scholars: Clockwise, starting with upper left: Mary Agnes Balogun (Morgan State), Mickayla Bacorn (University of Maryland, Baltimore County), Cassandra Olivas (California State University Stanislaus), and Amy Wu Wu (University of Puerto Rico-Mayaguez)

These students were part of RISE at Rutgers, a nationally acclaimed summer research program for outstanding undergraduates from diverse backgrounds. Scholars participate in cutting-edge research in the biological, physical, and social/ behavioral sciences, math, engineering, and exciting interdisciplinary areas under the guidance of carefully matched faculty mentors.

All four students finished their program by presenting their work at the 2021 American Crystallographic Association virtual meeting.

  • Mickayla Bacorn, Biochemical analysis and review of the active site evolution of SARS-CoV-2 and other coronaviruses
  • MaryAgnes Balogun, Understanding the active site of the SARS-CoV-2 papain-like proteinase (PLPro)
  • Cassandra Olivas, Using data mining to identify variations within the proteases of Coronaviridae
  • Amy Wu Wu, Bioinformatics and 3D Structural Analysis of the Coronavirus Main Protease Active Site Diversity

Amy and Mickayla's posters were each recognized with a Pauling Poster Prize. The Pauling Poster Prize was established by the ACA and is supported by member contributions, to honor Linus Pauling. Pauling was one of the pioneers in American structural research and was a very supportive member of the ACA for many years.

Amy and Cassandra were supported by an NSF REU to the RCSB PDB.


Bringing Molecular Structure to Life

09/09/2021

EMBL will host a virtual symposium on October 20-22, 2021 celebrating 50 years of the PDB.

Registration deadline is September 29.

Session Topics

  • Structural biology and applications in health and the environment
  • RNA/DNA molecular machines
  • The next 50 years: Genomics meets structural biology
  • Latest advances
  • The next 50 years: Future perspectives (part 1)
  • The next 50 years: Future perspectives (part 2)

Speakers

  • Bissan Al-Lazikani, The Institute of Cancer Research, UK
  • Cheryl H. Arrowsmith, University Health Network, Canada
  • M. Madan Babu, St. Jude Children‘s Research Hospital, USA
  • Drew Berry, Walter and Eliza Hall Institute of Medical Research, Australia
  • Wah Chiu, Stanford University, USA
  • Patrick Cramer, Max Planck Institute for Biophysical Chemistry, Germany
  • Petra Fromme, Arizona State University, USA
  • Donald Hilvert, ETH Zurich, Switzerland
  • Martin Jinek, University of Zurich, Switzerland
  • John Jumper, DeepMind, UK
  • Julia Mahamid, EMBL Heidelberg, Germany
  • Christine Orengo, University College London, UK
  • Lori A. Passmore, MRC Laboratory of Molecular Biology, UK
  • Jane Shelby Richardson, Duke University School of Medicine, USA
  • David Stuart, University of Oxford, UK
  • Nicolas Thomä, Friedrich Miescher Institute for Biomedical Research, Switzerland
  • Janet Thornton, EMBL-EBI Hinxton, UK
  • Sameer Velankar, EMBL-EBI Hinxton, UK

Panel Chair

  • Peter Rosenthal, The Francis Crick Institute, UK

Organizers

  • Stephen Cusack, EMBL Grenoble, France
  • Gerard Kleywegt, EMBL-EBI, UK
  • Christoph Mueller, EMBL Heidelberg, Germany
  • Christine Orengo, University College London, UK
  • Janet Thornton, EMBL-EBI, UK
  • Sameer Valenkar, EMBL-EBI, UK
  • Matthias Wilmanns, EMBL Hamburg, Germany


Poster Prize Awarded at ISMB/ECCB

08/31/2021

At this year's Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational Biology, the RCSB PDB Poster Prize award went to Tsukasa Nakamura.

Tsukasa NakamuraTsukasa Nakamura

Towards protein interface prediction using SE(3)-Transformer
Tsukasa Nakamura, JSPS(PD)/Tohoku University, Japan

Many thanks to judges Jose Duarte and Joan Segura (RCSB PDB) and to Steven Leard (ISMB) for his continued support.


Poster Prize Awarded at ACA

08/24/2021

At this year's American Crystallographic Association's Annual Meeting, the RCSB PDB Poster Prize award went to Karthik Srinivasan.

Karthik SrinivasanKarthik Srinivasan

Structural analysis of the Toc75 Potra domains from Pisum sativum
Karthik Srinivasan, Nicholas Noinaj (Purdue University), Srinivas Chakravarthy (Illinois Institute of Technology), Satchal Erramilli (The University of Chicago), Adrian Gonzalez (Molecular Templates Inc.)

The judges also awarded an Honorable Mention to Brenna Norton-Baker for

A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip
Brenna Norton-Baker (University of California, Irvine, UCI), Pedram Mehrabi (Universität Hamburg), David von Stetten (EMBL), Hendrik Schikora (Max Planck Institute for the Structure and Dynamics of Matter, MPSD), Ashley O. Kwok (UCI), Rachel W. Martin (UCI), R. J. Dwayne Miller (University of Toronto), Eike C. Schulz (Universität Hamburg)

Brenna Norton-BakerBrenna Norton-Baker

Many thanks to Poster Prize Chairs Sara N. Andres (McMaster University) and Tiffany Kinnibrugh (Argonne National Laboratory) and the judges: Jan Abendroth (UCB BioSciences), Christopher Berndsen (James Madison University), Jennifer Bridwell-Rabb (University of Michigan), Rafael M. Couñago (SGC-UNICAMP)


PDB50 at ACS August 25

08/17/2021

The Fall 2021 ACS meeting will be hybrid.The Fall 2021 ACS meeting will be hybrid.

Celebrate PDB50 at the Fall 2021 ACS Meeting with a session on Understanding Enzyme Function in 3D: Celebrating 50 Years of the Protein Data Bank.

All times shown are are listed in Eastern Daylight Time (EDT) on Wednesday August 25, 2021.

2:00 Introductory Remarks
2:05 The winding road from G-quadruplexes to telomerase, Juli Feigon (UCLA)
2:45 Enhanced exploration of small-molecule ligands bound to proteins and nucleic acids, Stephen K. Burley (Rutgers University and UCSD)
3:10 Mechanistic insights into the cleavage and polyadenylation machinery, Lori Passmore (University of Cambridge)
3:35 Vive la difference! The synergies and differences between the PDB and the CSD, Jason Cole (CCDC)
4:00 Break


4:30 Beyond static snapshots of protein structure: The role of dynamics in function, George Phillips Jr. (Rice University)
5:10 Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the COVID-19 pandemic, Sagar Khare (Rutgers)
5:35 Cracking the phosphatase code: Holoenzyme formation, regulatory protein binding and susbtrate dephosphorylation by the phosphoprotein phosphatase family, Rebecca Page (Brown)
6:00 Small molecules targeting COVID-19 in an evolving landscape of publishing and peer review, James Fraser (UCSF)
6:30 Break


7:00 Watching metalloenzymes at work, Amie Boal (Penn State)
7:25 Time travel to the past and future – evolution of energy landscapes for enzymes catalysis, Dorothee Kern (Brandeis)
7:50 Structure, mechanism, and inhibition of class IIb histone deacetylases, David Christianson (Harvard)
8:15 Truth sometimes triumphs: The history of structural enzymology, Gregory Petsko (Brandeis)
8:55 Closing Remarks

Visit ACS for registration information.

This symposium was organized by Carmen Nitsche (CCDC), and Steven C. Almo (Albert Einstein College of Medicine), and Stephen K. Burley (RCSB PDB).


Impact of PDB Structures on Anti-Cancer Drug Approvals

08/10/2021

A new flyer highlights the Impact of PDB Structures on Anti-Cancer Drug Approvals (PDF).

For more, see

Impact of the Protein Data Bank on antineoplastic approvals
(2020) Drug Discovery Today 25:837-850 doi: 10.1016/j.drudis.2020.02.002

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VAX Paintings

08/03/2021

Some of the Molecular Landscapes by David Goodsell explore the molecular basis of vaccines.

Immunological Synapse, Influenza Vaccine, and Poliovirus Neutralization are part of the VAX series. A painting of the SARS-CoV-2 mRNA Vaccine is also available.

These paintings are designed to be accurate representations of the biological processes, but also serve as a celebration of a miracle of modern medicine.

The watercolor paintings of David S. Goodsell integrate information from structural biology, microscopy and biophysics to simulate detailed views of the molecular structure of living cells. Proteins, nucleic acids, and lipid membranes are shown; small molecules, ions, and water are omitted for clarity.

<I>SARS-CoV-2 mRNA Vaccine</I>, 2020<BR>
 Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: <a href="http://doi.org/10.2210/rcsb_pdb/goodsell-gallery-027">10.2210/rcsb_pdb/goodsell-gallery-027</a>SARS-CoV-2 mRNA Vaccine, 2020
Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-027


PDB50: Function Follows Form

07/26/2021

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The 2021 ACA Meeting Transactions Symposium Function Follows Form: Celebrating the 50th Anniversary of the Protein Data Bank celebrates this golden anniversary.

Friday July 30 Speakers (12:00 - 3:00pm ET)

  • Cynthia Wolberger - Johns Hopkins, Baltimore, MD
  • Mike Martynowycz - HHMI/UCLA
  • John Rubinstein - Sick Kid’s Hospital, Toronto, Canada
  • Squire J. Booker - Penn State, State College, PA
  • Rafael M. Couñago- SGC/UNICAMP, Brazil
  • Erica Ollman Saphire - La Jolla Institute for Immunology, La Jolla, CA

Saturday July 31 Speakers (11:00 - 3:30pm ET)

  • Wayne A. Hendrickson - Columbia, New York, NY
  • Wladek Minor - University of Virginia
  • Chris Sander - Harvard Medical School, Boston, MA
  • Eva Nogales - UC Berkeley/HHMI, Berkeley, CA
  • Andrej Sali - RCSB PDB/UCSF, San Francisco, CA

Each day will end with a Panel Discussion: Leaning In – PDB in the Next 50 Years.


Other presentations by RCSB PDB student researchers and biocurators will include

Saturday, July 31 (4:00 - 5:00pm ET): Poster Session 1

  • Mickayla Bacorn, Biochemical analysis and review of the active site evolution of SARS-CoV-2 and other coronaviruses
  • MaryAgnes Balogun, Understanding the active site of the SARS-CoV-2 papain-like protease (PLPro)
  • Amy Wu Wu, Bioinformatics and 3D Structural Analysis of the Coronavirus Main Protease Active Site

Sunday, August 1 (4:00 - 5:00pm ET): Poster Session 2

  • Ethan Cartagena, PDB-101 Video Challenge: Creating a Winning Entry
  • Justin Flatt, The next generation RCSB.org
  • Brian Hudson, RCSB Protein Data Bank: Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive
  • Yuhe Liang, Trends in macromolecular structure data across 50 years of the PDB
  • Cassandra Olivas, Using data mining to identify variations within the proteases of Coronaviridae

Tuesday, August 3 (12:00 - 3:00pm ET): Session 2.2.2, Computing & Data Management

  • Gregg Crichlow, The Life and Times of the PDB Format - Looking Towards the Future with mmCIF


Summer Newsletter Published

07/15/2021

The Summer 2021 issue of the RCSB PDB Newsletter is now online.

This issue highlights PDB50 anniversary celebrations; consistent format for PDB data; sequence redundancy statistics; and more.

Published quarterly, each <a href="http://pdb101.rcsb.org/learn/education-corner">Education Corner</a> describes of how community members use the PDB and related resources.  Contact <a href="mailto:info@rcsb.org">info@rcsb.org</a> to contribute.Published quarterly, each Education Corner describes of how community members use the PDB and related resources. Contact info@rcsb.org to contribute.

The Education Corner by Dr Yinka Olatunji-Ojo describes Expanding Online Educational Resources at the CCDC.

Sign up to receive electronic updates each quarter.


Molecular Landscapes

07/06/2021

Whale muscles contain many myoglobin molecules (red) to store oxygen during their deep dives. This cross section shows the space between two muscle sarcomeres, which are shown at right and left with actin thin filaments in yellow and myosin thick filaments in tan. The space also includes many glycolytic enzymes and other other enzymes involved in energy production (blue) and glycogen granules (purple). A tubule of the sarcoplasmic reticulum is shown at the bottom, with many calcium pumps (blue molecules in the membrane) and calcium storage proteins (green) that concentrate calcium inside, for use in control of muscle contraction.

This painting was created as part of the celebration of the 50th anniversary of the Protein Data Bank.

This painting is part of PDB-101's SciArt gallery of Molecular Landscapes by David S. Goodsell.


PDB50 at ACS August 25

06/22/2021

The Fall 2021 ACS meeting will be hybrid.The Fall 2021 ACS meeting will be hybrid.

Celebrate PDB50 at the Fall 2021 ACS Meeting with a session on Understanding Enzyme Function in 3D: Celebrating 50 Years of the Protein Data Bank.

All times shown are are listed in Eastern Daylight Time (EDT) on Wednesday August 25, 2021.

2:00 Introductory Remarks
2:05 The winding road from G-quadruplexes to telomerase, Juli Feigon (UCLA)
2:45 Enhanced exploration of small-molecule ligands bound to proteins and nucleic acids, Stephen K. Burley (Rutgers University and UCSD)
3:10 Mechanistic insights into the cleavage and polyadenylation machinery, Lori Passmore (University of Cambridge)
3:35 Vive la difference! The synergies and differences between the PDB and the CSD, Jason Cole (CCDC)
4:00 Break


4:30 Beyond static snapshots of protein structure: The role of dynamics in function, George Phillips Jr. (Rice University)
5:10 Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the COVID-19 pandemic, Sagar Khare (Rutgers)
5:35 Cracking the phosphatase code: Holoenzyme formation, regulatory protein binding and susbtrate dephosphorylation by the phosphoprotein phosphatase family, Rebecca Page (Brown)
6:00 Small molecules targeting COVID-19 in an evolving landscape of publishing and peer review, James Fraser (UCSF)
6:30 Break


7:00 Watching metalloenzymes at work, Amie Boal (Penn State)
7:25 Time travel to the past and future – evolution of energy landscapes for enzymes catalysis, Dorothee Kern (Brandeis)
7:50 Structure, mechanism, and inhibition of class IIb histone deacetylases, David Christianson (Harvard)
8:15 Truth sometimes triumphs: The history of structural enzymology, Gregory Petsko (Brandeis)
8:55 Closing Remarks

Visit ACS for registration information.

This symposium was organized by Carmen Nitsche (CCDC), and Steven C. Almo (Albert Einstein College of Medicine), and Stephen K. Burley (RCSB PDB).


Guide to Understanding PDB Data: Carbohydrates

06/15/2021

Figure 2. Examples of carbohydrates in the PDB: the coronavirus spike protein (left; 7kip) with many sites of glycosylation in gray; a fragment of heparin (center; 3irl), shown with a ball-and-stick representation; and cholera toxin bound to a small fragment of O-type blood glycans (right, 5elb), with the glycans shown using SNFG representation.  <a href="https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/exploring-carbohydrates-in-the-pdb-archive">More on carbohydrates at PDB-101.</a>Figure 2. Examples of carbohydrates in the PDB: the coronavirus spike protein (left; 7kip) with many sites of glycosylation in gray; a fragment of heparin (center; 3irl), shown with a ball-and-stick representation; and cholera toxin bound to a small fragment of O-type blood glycans (right, 5elb), with the glycans shown using SNFG representation. More on carbohydrates at PDB-101.

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 carbohydrates are represented in the PDB archive. Topics in this article include:

  • General Overview
  • Importance of Carbohydrates in Biology
  • Representing Carbohydrates
  • How Carbohydrates are Specified in PDB Entries
  • Finding carbohydrates in the archive
  • The "Oligosaccharides" Section of the Structure Summary Page
  • Viewing Carbohydrates in Mol*


Congratulations to Poster Prize Winners

06/08/2021

Poster Prize awardeesPoster Prize awardees

At the inaugural PDB50 meeting, ~275 posters were presented (Abstracts Day 1 | Day 2); 209 of these presentations were considered for poster prize awards.

  • Best in High School: Nicholas Mamisashvili, Shelter Island High School, Molecular Dynamics Simulation of 6PEY.pdb a Novel Mutation in the Enzyme Methylenetetrahydrofolate Reductase
  • Best in Undergraduate: Ijeoma Okoye, Vassar College, X-ray and Antioxidant Determination of Butein and 2’,4’-dihydroxy-3,4-dimethoxychalcone to Examine their Antimalarial Activity by Binding to Falcipain-2
  • Best in Graduate: Daniel Sultanov, New York University, Mining for functional ribosomal variants in Saccharomyces cerevisiae
  • Best in Postdoctoral Scholars: Seda Kocaman, National Institute of Environmental Health Sciences, Different ATP binding states of the essential AAA (ATPases Associated with various Activities)-ATPase Rix7 facilitate substrate translocation in ribosome biogenesis

Many thanks to the poster prize judges:

  • BMRB: Hamid Eghbalnia
  • PDBe: Genevieve Evans, John Berrisford
  • PDBj: Genji Kurisu
  • UConn: Bing Hao, Irina Bezsonova, Melissa Caimano
  • University of Naples: Luigi Di Costanzo
  • RCSB: Brian Hudson, Brinda Vallat, Cathy Lawson, Chenghua Shao,
  • David Goodsell, Dennis Piehl, Ezra Peisach, Helen Berman, Irina Persikova, Joan Segura, Justin Flatt, Rachel Kramer Green, Stephen Burley, Yuhe Liang, Zukang Feng
  • RIT: Paul Craig

wwPDB is celebrating the 50th Anniversary of the PDB throughout 2021 with symposia, materials, and more.


Education Corner: Exploring the Structure-Function Relationship

06/01/2021

The Spring 2021 issue of the RCSB PDB Newsletter is now online.

In the Education Corner, Maria Voigt (RCSB PDB) describes Exploring the Structure-Function Relationship with Digital and Physical 3D Models of Proteins. Maria highlights PDB-101's 3D print collection that is designed to be interactive.

Other articles in this issue highlight PDB50 anniversary celebrations; the CellPAINT contest (submit images by May 1); new search tools; and more.


How the Protein Data Bank Changed Biology

05/25/2021

Journal of Biological Chemistry (JBC) has published a collection of reviews in celebration of PDB50.

This issue, edited by Lila Gierasch (JBC) and Helen Berman (wwPDB Foundation, RCSB PDB), contains 17 reviews highlighting the impact of the PDB archive across biological chemistry.

JBC was one of the first journals to require PDB deposition of structural data reported in accepted articles. In addition, more structures in the PDB have been published in JBC than in any other journal.


Evolution of PDB-101

05/21/2021

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The CSD Educators Blog hosted at the Cambridge Crystallographic Data Centre posts stories about educational journeys and how the Cambridge Structural Database can be key to learning.

Established in 1965, the CSD is the world’s repository for small-molecule organic and metal-organic crystal structures. Containing over one million structures from x-ray and neutron diffraction analyses, this unique database of accurate 3D structures has become an essential resource to scientists and a tool for education.

The latest article in the blog series looks at Evolution of PDB-101: Molecular Explorations Through Biology and Medicine.

This year, RCSB PDB and wwPDB are celebrating the golden anniversary of the PDB with symposia, events, and related resources.

2021 marks another milestone important to RCSB PDB: the 10th anniversary of PDB-101, RCSB PDB’s online portal for teachers, students, and the general public to promote exploration in the world of proteins and nucleic acids.

Visit the CSD Educators Blog for more.


Award-Winning Videos on Molecular Mechanisms of Drugs for Mental Disorders

05/18/2021

High school students are excellent science communicators. The submitted entries in this year's Video Challenge demonstrate tremendous creativity and used many storytelling approaches to communicate the Molecular Mechanisms of Drugs for Mental Disorders.

Congratulations to the 2021 Prize Winners

  • First Place: Inhibiting Acetylcholine Destruction to Combat Alzheimer's Disease by Ethan Cartagena from Peninsula Liberty Academy, San Carlos, CA (Team advisor: Deanne Cartagena)
  • Second Place: SSRIs: Sustaining Smiles by Khushi Desai, Gabrielle Bailey, Trisha Kopparthi, and Tanvi Singh of West Windsor-Plainsboro High School South, West Windsor, NJ (Team advisor: Matthew Foret)
  • Third Place: Method in Madness: A Guide to Schizophrenia by Smita Rosemary, Rachel Yan, and Alyssa Wu of East Brunswick High School, East Brunswick, NJ (Team advisor: Anne Sanelli)
  • Viewers’ Choice: The Late Night Study Session: Derek's Depression Dream by Natasha Kulviwat, Derek Minn, and He-Hanson Xuan of Jericho High School, Jericho, NY (Team advisor: Mrs. Samantha Sforza)

Our panel of expert judges (Margaret A. Franzen (MSOE Center for BioMolecular Modeling), Steven W. Levison (New Jersey Medical School, Rutgers University), and Christine D. Young (University of Illinois at Chicago) scored the videos based on Quality of Storytelling (20%), Quality of Science Communication (30%), Quality of Public Health Message (10%), Originality and Creativity (20%), Quality of Production (10%), and Proper Accreditation (10%).

The general public voted for the Viewer's Choice Award.

Many thanks to the expert judges, students, teachers, parents, and voters who made this exciting competition happen!


CellPAINT Contest Winners

05/12/2021

CellPAINT can be used to create drawing pictures of cellular and viral systems. The Scripps Research Center for Computational Structural Biology (CCSB) in association with RCSB PDB hosted an coronavirus image contest created using CellPAINT in the categories of PDB50 and vaccines.

Best in Celebrating PDB

Happy 50th birthday to PDB! by Irina Bezsonova (University of Connecticut).Happy 50th birthday to PDB! by Irina Bezsonova (University of Connecticut).

Best in Celebrating Vaccines

COVID-19 may keep us distanced, but we can still celebrate! Our immune system is our natural defense system, and vaccines will strengthen us (Kirsten Fertuck, Northeastern University)<P>COVID-19 may keep us distanced, but we can still celebrate! Our immune system is our natural defense system, and vaccines will strengthen us (Kirsten Fertuck, Northeastern University)

Many thanks to everyone who participated.


Vote Now for the Viewer's Choice Award

05/07/2021

RCSB PDB challenged high school students to create short videos that tell stories about the Molecular Mechanisms of Drugs for Mental Disorders.

Watch the challenge entries online and cast your vote for your favorite video by May 10.

Award winners will be announced on RCSB.org and PDB101.rcsb.org on May 18, 2021.


Explore the History of the PDB

04/27/2021

Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive (see wwpdb.org/pdb50 and rcsb.org/pdb50).

Explore a historical overview of the PDB, including a timeline that tracks highlights from the PDB and the structural biology community.


Annual Report Published

04/24/2021

Download the 2020 Annual Report (PDF) for an overview of recent Deposition/Biocuration, Archive Management/Access, Data Exploration, and Outreach/Education activities.

This review highlights many RCSB PDB accomplishments, PDB structures and the pandemic, and celebrating 50 years of the PDB archive.

These bulletins provide a yearly snapshot of RCSB PDB activities and the state of the PDB archive.


EXTENDED: Enter the 2021 CellPAINT Contest by May 6

04/24/2021

Show us illustrations inspired by vaccines and by 50 years of the PDB coronavirus with a new version of CellPAINT. The Scripps Research Center for Computational Structural Biology (CCSB) in association with RCSB PDB is hosting an image contest. There are two categories: Science of Vaccines and 50 Years of PDB.

Images for the <B><I>Science of Vaccines</I></B> category need to be accurate and present aspects of structure and biology--create something that helps us understand vaccines and how they work.Images for the Science of Vaccines category need to be accurate and present aspects of structure and biology--create something that helps us understand vaccines and how they work.
In the <B><I>50 Years of PDB</I></B> category, let your creativity run wild with any topic that celebrates 50 years of access to biological macromolecules in the Protein Data Bank archive--create something that amazes and inspires.In the 50 Years of PDB category, let your creativity run wild with any topic that celebrates 50 years of access to biological macromolecules in the Protein Data Bank archive--create something that amazes and inspires.

Suggested resources include Molecule of the Month articles on Adenovirus, Human Papillomavirus and Vaccines, and Measles Virus Proteins; Resources to Fight the COVID-19 Pandemic: SARS-CoV-2 mRNA Vaccine and Passive Immunization with Convalescent Antibodies; mRNA vaccines - a new era in vaccinology (Nat Rev Drug Discov 2018); and PDB-101 resources on viruses.

Suggested resources include PDB50 materials, Structural Biology and Nobel Prizes, and Molecule of the Month articles on PDB Pioneers and Twenty Years of Molecules.

For this contest, you can submit images created using the web-based program or the stand-alone version.

A CellPAINT tutorial provides information on how to create images using the program.

Information about new molecules added to CellPAINT for drawing illustrations of mRNA vaccines like the ones being used to fight COVID-19 is available.

Contest Overview

  • The contest is open to all, with one entry per person in each category.
  • Submitted should be still images submitted in a familiar format (jpg, tiff, etc), that use CellPAINT in some or all of the image creation.
  • The contest will be judged by members of the CCSB and RCSB PDB.
  • Participants are encouraged to share their entries online with the hashtags #VaccinesByCellPAINT or #CelebratePDB, but need to submit using the online form to be considered.

Submit by May 7, 2021

Option 1: I have a Google Account

Option 2: I don't have a Google account


Winners of each category will be awarded:

A set of PDB-themed cards created by David S. Goodsell.A set of PDB-themed cards created by David S. Goodsell.

CellPAINT

CellPAINT is software for drawing pictures of cellular and viral systems, similar to a traditional digital paint program. The shapes and sizes of molecules are based on atomic structures taken from the Protein Data Bank, and the program allows you to build membranes, add membrane-bound proteins, and fill the inside and outside with soluble proteins and other molecules (more information).

About the RCSB PDB and PDB-101

RCSB.org enables breakthroughs in scientific and biomedical research and education through tools and resources built on top of the PDB archive of 3D proteins and nucleic acids. RCSB PDB and the wwPDB are celebrating the 50th Anniversary of the PDB with symposia, materials, and more.


Celebrate DNA Day on April 25

04/23/2021

DNA Day commemorates the completion of the Human Genome Project in 2003 and the discovery of DNA's double helix in 1953. Celebrate by:

DNA and RNA are the cell’s way of storing and deploying genetic information. Structural biology is revealing that some nucleic acids also fold to form complex molecular machines. Guided by these structures, nanotech scientists are building new machines composed of nucleic acid. <a href="http://pdb101.rcsb.org/browse/nucleic-acids">Learn more at PDB-101</a>DNA and RNA are the cell’s way of storing and deploying genetic information. Structural biology is revealing that some nucleic acids also fold to form complex molecular machines. Guided by these structures, nanotech scientists are building new machines composed of nucleic acid. Learn more at PDB-101


Register for PDB50 by May 1

04/18/2021

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Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive (wwpdb.org/pdb50).

The inaugural symposium will be held virtually on May 4-5, 2021.

The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day. The event will be recorded and made available to registered participants after the meeting.

Students and postdoctoral fellows are especially encouraged to attend and will be eligible for poster awards.

Register by May 1 at https://www.asbmb.org/meetings-events/pdb50.

Speakers

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Scientific Software Developers and Postdocs

04/15/2021

Join RCSB PDB to design, develop, & deploy modern web and data applications & complex user interfaces. Help accelerate research and training in biology, medicine, & related disciplines. Positions at Rutgers and SDSC/UCSD.

RCSB PDB team pictured at the January 2020 <I>Cloud Technologies Best Practices</I> hosted by the Institute for Quantitative Biomedicine at Rutgers, The State University of New Jersey.RCSB PDB team pictured at the January 2020 Cloud Technologies Best Practices hosted by the Institute for Quantitative Biomedicine at Rutgers, The State University of New Jersey.


Spring Newsletter Published

04/13/2021

The Spring 2021 issue of the RCSB PDB Newsletter is now online.

This issue highlights PDB50 anniversary celebrations; the CellPAINT contest (submit images by May 1); new search tools; and more.

The Education Corner by RCSB PDB's Maria Voigt Explores the Structure-Function Relationship with Digital and Physical 3D Models of Proteins.

Sign up to receive electronic updates each quarter.


Developers: HTTPS enforcement starts May 10

04/09/2021

RCSB PDB APIs, RCSB.org, and PDB101.rcsb.org will enforce use of the secure HTTPS protocol starting May 10, 2021. HTTP Strict Transport Security headers will be implemented.

RCSB.org data and services have supported HTTPS protocol since 2017, but with this change all users will be redirected to HTTPS to guarantee secure communication.

Programmatic users are encouraged to switch to HTTPS as soon as possible. Not all HTTP clients will necessarily follow redirects automatically.

Individual website users should not be impacted, as modern web browsers will redirect automatically.


Download Molecular Landscapes

04/06/2021

Acknowledgement: David S. Goodsell, RCSB Protein Data Bank doi: <a href="http://pdb101.rcsb.org/sci-art/goodsell-gallery/respiratory-droplet">10.2210/rcsb_pdb/goodsell-gallery-024</a>Acknowledgement: David S. Goodsell, RCSB Protein Data Bank doi: 10.2210/rcsb_pdb/goodsell-gallery-024

This painting by David S. Goodsell shows a cross section through a small respiratory droplet, like the ones that are thought to transmit SARS-CoV-2. The virus is shown in magenta, and the droplet is also filled with molecules that are present in the respiratory tract, including mucins (green), pulmonary surfactant proteins and lipids (blue), and antibodies (tan). The painting was created as part of the show New Ways of Living with SciCommMake.

Goodsell's molecular landscapes are available from PDB-101 in a special SciArt Digital Archive. These watercolor paintings integrate information from structural biology, microscopy and biophysics to simulate detailed views of the molecular structure of living cells. These illustrations are free for use under CC-BY-4.0 license. Acknowledgement should be given as indicated for each illustration.


Enter the 2021 CellPAINT Contest by May 1

04/01/2021

Show us illustrations inspired by vaccines and by 50 years of the PDB coronavirus with a new version of CellPAINT. The Scripps Research Center for Computational Structural Biology (CCSB) in association with RCSB PDB is hosting an image contest. There are two categories: Science of Vaccines and 50 Years of PDB.

Images for the <B><I>Science of Vaccines</I></B> category need to be accurate and present aspects of structure and biology--create something that helps us understand vaccines and how they work.Images for the Science of Vaccines category need to be accurate and present aspects of structure and biology--create something that helps us understand vaccines and how they work.
In the <B><I>50 Years of PDB</I></B> category, let your creativity run wild with any topic that celebrates 50 years of access to biological macromolecules in the Protein Data Bank archive--create something that amazes and inspires.In the 50 Years of PDB category, let your creativity run wild with any topic that celebrates 50 years of access to biological macromolecules in the Protein Data Bank archive--create something that amazes and inspires.

Suggested resources include Molecule of the Month articles on Adenovirus, Human Papillomavirus and Vaccines, and Measles Virus Proteins; Resources to Fight the COVID-19 Pandemic: SARS-CoV-2 mRNA Vaccine and Passive Immunization with Convalescent Antibodies; mRNA vaccines - a new era in vaccinology (Nat Rev Drug Discov 2018); and PDB-101 resources on viruses.

Suggested resources include PDB50 materials, Structural Biology and Nobel Prizes, and Molecule of the Month articles on PDB Pioneers and Twenty Years of Molecules.

For this contest, you can submit images created using the web-based program or the stand-alone version.

A CellPAINT tutorial provides information on how to create images using the program.

Information about new molecules added to CellPAINT for drawing illustrations of mRNA vaccines like the ones being used to fight COVID-19 is available.

Contest Overview

  • The contest is open to all, with one entry per person in each category.
  • Submitted should be still images submitted in a familiar format (jpg, tiff, etc), that use CellPAINT in some or all of the image creation.
  • The contest will be judged by members of the CCSB and RCSB PDB.
  • Participants are encouraged to share their entries online with the hashtags #VaccinesByCellPAINT or #CelebratePDB, but need to submit using the online form to be considered.

Submit by May 1, 2021

Option 1: I have a Google Account

Option 2: I don't have a Google account


Winners of each category will be awarded:

A set of PDB-themed cards created by David S. Goodsell.A set of PDB-themed cards created by David S. Goodsell.

CellPAINT

CellPAINT is software for drawing pictures of cellular and viral systems, similar to a traditional digital paint program. The shapes and sizes of molecules are based on atomic structures taken from the Protein Data Bank, and the program allows you to build membranes, add membrane-bound proteins, and fill the inside and outside with soluble proteins and other molecules (more information).

About the RCSB PDB and PDB-101

RCSB.org enables breakthroughs in scientific and biomedical research and education through tools and resources built on top of the PDB archive of 3D proteins and nucleic acids. RCSB PDB and the wwPDB are celebrating the 50th Anniversary of the PDB with symposia, materials, and more.


Molecular Landscapes: E. coli

03/23/2021

A new painting by David S. Goodsell illustrates a cross-section through an Escherichia coli cell. The image is available for download from the Molecular Landscapes SciArt Gallery.

This painting is an update of an earlier E. coli painting from 1999, incorporating abundant new data that has been gathered since then, including proteomics information and many amazing new structures.

Goodsell's molecular landscapes are available from PDB-101 in a special SciArt Digital Archive. These watercolor paintings integrate information from structural biology, microscopy and biophysics to simulate detailed views of the molecular structure of living cells. These illustrations are free for use under CC-BY-4.0 license. Acknowledgement should be given as indicated for each illustration.


Submit Abstracts for PDB50

03/07/2021

Throughout 2021, RCSB PDB and the wwPDB will celebrate the 50th anniversary of the PDB archive (wwpdb.org/pdb50 and wwpdb.org/pdb50).

The inaugural symposium will be held virtually on May 4-5, 2021.

The online sessions will take place between 11 a.m. – 4:30 p.m. ET each day. The event will be recorded and made available to registered participants after the meeting.

Students and postdoctoral fellows are especially encouraged to attend and will be eligible for poster awards.

Abstract submission and reduced registration rates end March 15.
Register at https://www.asbmb.org/meetings-events/pdb50.

Speakers

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More than 1,000 SARS-CoV-2 Coronavirus Protein Structures Available

03/02/2021

With this week's update, 1,018 SARS-CoV-2-related structures are now freely available from the Protein Data Bank.

The first SARS-CoV-2 structure, a high-resolution crystal structure of the coronavirus main protease (PDB 6lu7), was released early in the pandemic on February 5, 2020.

Since then, structural biologists have visualized most of the SARS-CoV-2 proteome, including the spike protein binding to its ACE2 receptor and neutralizing antibodies, and the main protease, the papain-like proteinase, and other promising drug discovery targets. All of the structures and related data are available for exploration from wwPDB partner websites: RCSB PDB, PDBe, PDBj, and BMRB.

Rapid public release of SARS-CoV-2 structure data has greatly increased our understanding of Covid-19, allowed direct visualization of emerging variants of the virus, and facilitated structure-guided drug discovery and reuse to combat infection. Open access to PDB structures has already enabled design of effective vaccines against SARS-CoV-2.

The response of the research community to the pandemic has highlighted the importance of open access to scientific data in real time. The wwPDB strives to ensure that 3D biological structure data remain freely accessible for all, while maintaining as comprehensive and accurate an archive as possible.

The impact of these 1018 structures and many more coronavirus protein structures to come stands as a testament to the importance of open access to structural biology research data.

Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: <a href="http://pdb101.rcsb.org/sci-art/goodsell-gallery/respiratory-droplet">10.2210/rcsb_pdb/goodsell-gallery-024</a>. <BR><a href="http://pdb101.rcsb.org/browse/coronavirus">Visit PDB-101 for related educational materials.</a>Illustration by David S. Goodsell, RCSB Protein Data Bank; doi: 10.2210/rcsb_pdb/goodsell-gallery-024.
Visit PDB-101 for related educational materials.


High School Students: Submit Videos By April 27

02/25/2021

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The brain orchestrates everything we do, sending signals through the nervous system to control different parts of our body. The brain is also the home of our thoughts and consciousness, as neurons process the input from our senses and store what they find as memories. Sometimes this input is not processed right. This can be modulated by the drugs prescribed by the doctors to amplify or to soften the neuronal signal.

High school students can help increase awareness by participating in the 2021 Video Challenge for High School Students on Molecular Mechanisms of Drugs for Mental Disorders.

Submit your entry on or before April 27, 2021. Visit PDB-101 for contest details, resources, guidelines, and the panel of expert judges.


Join Us at the Feb 24 Biophysical Society Job Fair

02/21/2021

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Meet with team members to learn about open positions for Scientific Software Developers (Rutgers and UCSD), Postdoctoral Researchers (UCSD), and summer undergraduate researchers (virtually at Rutgers).

RCSB PDB is a world-renowned, scientific organization focused on serving technical, educational and other programmatic needs of scientific and research communities worldwide. RCSB.org serves millions of users in academia and industry. The RCSB PDB development team, located at UCSD/SDSC and Rutgers, creates leading edge web technologies targeted for scientific and educational audiences.

Join the RCSB PDB and participate in exciting projects with significant impact on the scientific community.

Can't attend the fair? Please Contact Us with any questions.

RCSB PDB Team in 2020RCSB PDB Team in 2020
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PDB50: Submit Posters by March 15

02/15/2021

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Throughout 2021, the wwPDB will be celebrating the 50th anniversary of the PDB archive.

The inaugural symposium will be held May 4-5, 2021 in an event hosted by the American Society for Biochemistry and Molecular Biology and organized by the wwPDB Foundation.

This celebration of the 50th anniversary of the founding of the Protein Data Bank as the first open access digital data resource in biology will include presentations from speakers from around the world who have made tremendous advances in structural biology and bioinformatics.

Attendees are encouraged to participate in the virtual poster session and exhibition hall. Students and postdoctoral fellows will be eligible for poster awards.

Register and submit abstracts by March 15th, 2021 for reduced rates.

Speakers will include:

  • Edward Arnold - Rutgers, The State University of New Jersey
  • Helen M. Berman - Rutgers, The State University of New Jersey and University of Southern California
  • Thomas L. Blundell - University of Cambridge
  • Alexandre M. J. J. Bonvin - Utrecht University
  • Stephen K. Burley - Rutgers, The State University of New Jersey and University of California San Diego
  • Wah Chiu - Stanford University
  • Johann Deisenhofer - University of Texas Southwestern Medical Center
  • Juli Feigon - University of California Los Angeles
  • Angela M. Gronenborn - University of Pittsburgh
  • Jennifer L. Martin - University of Wollongong
  • Stephen L. Mayo - California Institute of Technology
  • Zihe Rao - ShanghaiTech University and Tsinghua University
  • Hao Wu - Boston Children's Hospital and Harvard Medical School

The online sessions will take place between 11 a.m. – 4:30 p.m. EST each day. The event will be recorded and made available to registered participants after the meeting.

Sponsorship opportunities are available; please contact the wwPDB Foundation for more information.


Molecular Valentines

02/11/2021

Click on each image to expand.



PDB50 Backgrounds For Virtual Meetings

02/02/2021

The wwPDB created a 2021 calendar to celebrate the PDB's golden anniversary.

Each month's image is available to be used as a virtual meeting background.

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The inaugural symposium will be held May 4-5, 2021 in an event hosted by the American Society for Biochemistry and Molecular Biology and organized by the wwPDB Foundation. The online sessions will take place between 11 a.m. – 4:30 p.m. EST each day. The event will be recorded and made available to registered participants after the meeting.

Attendees are encouraged to participate in the virtual poster session and exhibition hall. Students and postdoctoral fellows will be eligible for poster awards.

Register and submit abstracts by March 15th, 2021 for reduced rates.


Powerful New Tools for Exploring 3D Structures

01/26/2021

A new article in Nucleic Acids Research uses SARS-CoV-2 structures to demonstrate redesigned RCSB.org features for exploring structural data.

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences
Nucleic Acids Research (2021) 49: D437–D451 doi: 10.1093/nar/gkaa1038

This tutorial and overview of the latest RCSB.org tools appears in the annual Database Issue of Nucleic Acids Research.

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Winter Newsletter Published

01/11/2021

The Winter 2021 issue of the RCSB PDB Newsletter is now online.

This issue highlights PDB50 anniversary celebrations; 2020 statistics; new search tools; Biocurator explores SARS-CoV-2 in VR; and more.

The Education Corner describes the 2020 ACA Transactions Symposium on Structural Science: New Ways to Teach the Next Generation.

Sign up to receive electronic updates each quarter.


Past news and events have been reported at the RCSB PDB website and past Newsletters.