Education Corner: Creating 3D Protein Models and Videos

05/20 

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In the Spring 2024 Newsletter, learn about Building and Animating Catalase in a High School Classroom . AP Biology students at John H. Pitman High School were tasked with creating animations depicting an active site in catalase and the mechanistic breakdown of two hydrogen peroxide molecules. These animations were created using pipe cleaners, clay, toothpicks, and stop-motion cinematography. The data used to generate these animations were from RCSB Protein Data Bank resources, AlphaFold DB, and various scientific publications. This project represents a Science Technology Engineering Art and Math (STEAM) and Project Based Learning (PBL) approach to a common enzyme lab. Below is an anecdote depicting what the project was and meant to one of the students in the class.

Training Opportunities; a Python Package to Access the Search API; a new Cancer Molecular Animation; and more.

Published quarterly, each Education Corner describes of how community members use the PDB and related resources.
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News Index

• 12/17 PDB-101 Focus: Peak Performance

• 12/17 Paper Published: ZMPY3D

• 12/10 Model Proteins at the Science Olympiad

• 12/06 Structural Biology and Nobel Prizes

• 12/03 Watch the Webinar: Python Scripting for Molecular Docking

• 11/27 December 1: World AIDS Day

• 11/27 wwPDB News: Access SDF/MOL formatted CCD files from the PDB archive

• 11/25 Education Corner: Paper Nucleic Acid Models for Hands-on Education

• 11/21 PDB-101 Focus: Peak Performance

• 11/19 Paper Published: Using Augmented Reality

• 11/17 Nov 18-24: World Antimicrobial Awareness Week

• 11/14 Nov 17: WHO's Cervical Cancer Elimination Day of Action

• 11/13 November 14 is World Diabetes Day

• 11/11 Developers: Switch to Sequence Coordinates Service by May 31, 2025

• 11/10 Meet RCSB PDB at ABRCMS

• 11/05 Paper Published: IHMCIF

• 11/04 Take the Visualization User Survey and Win

• 10/31 wwPDB News: Deprecation of FTP File Download Protocol on November 1, 2024

• 10/29 wwPDB News: Poster Prize Awarded at The Protein Society

• 10/27 Meet RCSB PDB at SACNAS

• 10/25 Register for Upcoming Training Events

• 10/22 wwPDB News: Poster Prize Awarded at LACA

• 10/20 Interview with Director Emerita Helen Berman

• 10/18 Happy Birthday, PDB!

• 10/17 Happy Birthday, Irving Geis

• 10/16 wwPDB News: The Nobel Prize in Chemistry 2024

• 10/16 Register for the November 4 Mol* Virtual Office Hour

• 10/15 wwPDB News: wwPDB Data Release Policy on Public Preprint Archives

• 10/15 PDB-101 Focus: Peak Performance

• 10/10 Paper Published: MolViewSpec Toolkit

• 10/09 Register for the November 7 Virtual Office Hour on Supporting Extended PDB IDs

• 10/09 Explore Structural Biology with CSMs

• 10/08 wwPDB News: Annotation of Protein Modifications in the PDB

• 10/07 Fall Newsletter Published

• 10/02 wwPDB News: Access IHM structures at wwPDB DOI Landing Pages

• 09/30 Explore Inktober SciArt images

• 09/29 Register Now for Webinar: Unlock Rapid Analyses Across the Whole PDB Using BinaryCIF

• 09/25 Structural Biology and Nobel Prizes

• 09/25 Register for the October 8 Advanced Search Office Hour

• 09/24 Announcement and FAQ: EDMAPS.rcsb.org Shutdown October 16

• 09/23 Applications Open for Director

• 09/21 Watch the Webinar: Teaching Enzymology

• 09/20 Education Corner: Building Machines in the Classroom

• 09/17 Poster Prize Awarded at ACA 2024

• 09/17 wwPDB News: Deprecation of FTP File Download Protocol on November 1, 2024

• 09/17 Deprecation of ligand model coordinates in SDF format starting Dec 10

• 09/15 Celebrating National Postdoc Appreciation Week

• 09/12 Molecular Landscapes

• 09/08 PDB-101 Focus: Peak Performance

• 09/03 Poster Prize Awarded at ISMB 2024

• 08/28 wwPDB News: Biocurator Milestone: >10,000 Depositions Processed

• 08/27 Paper Published: Exploring protein 3D similarities via comprehensive structural alignments

• 08/26 Register for the Sept 18 Virtual Office Hour on Molecular Animations

• 08/21 Register for the Sept 12 Virtual Office Hour: Streamlining PDB Deposition

• 08/20 PDB-101 Focus: Peak Performance

• 08/14 Register for the Sept 9 Mol* Virtual Office Hour

• 08/14 wwPDB News: PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM)

• 08/13 August is National Immunization Awareness Month

• 08/05 Join our DevOps Team at Rutgers

• 07/30 August 2 is National Coloring Book Day

• 07/25 July 28 is World Hepatitis Day

• 07/23 PDB-101 Focus: Peak Performance

• 07/16 Paper Published: RCSB PDB supporting research and education worldwide

• 07/08 Summer Newsletter Published

• 07/03 Meet the RCSB PDB at ISMB

• 07/01 Meet the RCSB PDB at ACA

• 06/30 Postdocs: Join our Development Team in San Diego

• 06/30 Switch from MMTF to BCIF

• 06/28 Register for the July 9 Virtual Office Hour on APIs

• 06/27 Notice: NGL Viewer Deprecation

• 06/25 Paper Published: Cryo-EM Ligand Modeling Challenge

• 06/25 Register Now for Webinar on Teaching Enzymology

• 06/18 Register Now for Crash Course: Python Scripting for Molecular Docking

• 06/18 wwPDB News: Announcing the New PDBx/mmCIF User Guide

• 06/16 Paper Published on NextGen Archive

• 06/11 Register for the July 9 Virtual Office Hour on APIs

• 06/11 PDB-101 Focus: Peak Performance

• 06/06 wwPDB News: Biocurator Milestone: >10,000 Depositions Processed

• 06/04 Register for June 13 Virtual Office Hour: Generating DSN6 and MTZ Files

• 06/04 Molecular Origami: Build 3D Paper Models of Protein Domains

• 05/31 Register for the June 4th Webinar

• 05/27 Notice: NGL Viewer Deprecation

• 05/26 Explore the Structural Biology of Evolution

• 05/20 Education Corner: Creating 3D Protein Models and Videos

• 05/16 PDB-101 Focus: Peak Performance

• 05/14 Switch from MMTF to BCIF

• 05/13 Register for the June 3 Mol* Virtual Office Hour

• 05/09 Announcement: EDMAPS.rcsb.org Shutdown

• 05/08 wwPDB News: Poster Prize Awarded at DiscoverBMB

• 05/07 wwPDB News: Celia Schiffer Elected to National Academy of Sciences

• 05/05 Video: How Neurons Communicate

• 05/01 Register Now for a Webinar on Understanding PDB Validation: Which experimental structures should I rely on?

• 04/30 wwPDB News: Coming soon: Annotation of Protein Modifications in the PDB

• 04/30 Annual Report Published

• 04/23 April 24 to 30 is World Immunization Week

• 04/21 Celebrate DNA Day on April 25

• 04/18 April 22 is Earth Day

• 04/16 Spring Newsletter Published

• 04/14 Paper Published: Folding paper models of biostructures for outreach and education

• 04/09 Register Now for a Webinar on Understanding PDB Validation: Which experimental structures should I rely on?

• 04/08 wwPDB News: CASP16 Call for Targets

• 04/02 Video: Immunology and Cancer

• 04/01 Register Now for a Virtual Deep Dive into Computed Structure Model Exploration at RCSB.org

• 04/01 Paper Published on NMR Restraint Validation

• 03/31 Explore Mechanism and Catalytic Site Annotations

• 03/29 Take the EDMAPS.rcsb.org Survey

• 03/26 Education Corner: Bringing Proteins to Life

• 03/24 Register for the April 1 Mol* Virtual Office Hour

• 03/21 March 24 is World TB Day

• 03/20 Meet RCSB PDB at the #DiscoverBMB Meeting

• 03/17 Paper Published: Visualizing groups of PDB structures and CSMs

• 03/12 wwPDB News: Paper Published on CryoEM Archiving and Validation Recommendations

• 03/11 March 11-17: Brain Awareness Week

• 03/06 wwPDB News: Poster Prize Awarded at The Biophysical Society Meeting

• 02/29 March 4 is International HPV Awareness Day

• 02/27 February 29 is Rare Disease Day

• 02/27 wwPDB News: Latest Developments on the EMDB Published

• 02/25 Register for the March 28 Office Hour to Ask A Biocurator

• 02/23 wwPDB Preprint Published on NMR Restraint Validation

• 02/20 wwPDB Preprint Published on CryoEM Archiving and Validation Recommendations

• 02/16 PDB-101 Focus: Peak Performance

• 02/14 wwPDB Preprint Published on NextGen Archive

• 02/12 Use a Python Package to Access the RCSB PDB Search API

• 02/11 Molecular Valentines

• 02/06 Meet RCSB PDB at The Biophysical Society Meeting

• 02/01 February 4 is World Cancer Day

• 01/30 Notice: NGL Viewer Deprecation

• 01/30 Register for VIZBI 2024 (March 13–15)

• 01/24 Take the CSM User Survey and Win

• 01/19 Register for the February 13 Mol* Webinar

• 01/18 Undergrads: Spend your summer with RCSB PDB

• 01/16 Register for the February 5 RCSB.org Office Hour

• 01/15 Switch from MMTF to BCIF

• 01/10 Celebrate #NationalMilkDay

• 01/08 wwPDB News: Resources for Supporting the Extended PDB ID Format (pdb_00001abc)

• 01/08 Winter Newsletter Published

• 01/07 Applications Open for Director

• 01/04 Top Molecules of the Month in 2023

• 01/03 wwPDB News: Time-stamped Copies of PDB and EMDB Archives