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Python For Cheminformatics-Driven Molecular DockingThis workshop uses Python scripting to explore and compare small molecules that bind to the SARS-CoV2 main protease. Work is performed in a Google CoLab environment and involves a number of libraries heavily used for cheminformatics. |
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Streamlining Access to RCSB PDB APIs with PythonThis webinar introduces and demonstrates usage of the rcsb-api Python package which enables researchers to easily interact with RCSB PDB Search and Data API services. Using this toolkit, users can seamlessly integrate search and data retrieval tasks into computational workflows for custom analyses. |
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Seeing Bird Flu in 3D: Exploring Influenza A H5N1 Virus Protein Structures using RCSB.org ToolsViruses represent major threats to global health. Historically, pandemics of influenza, polio, smallpox, and many other viruses have spread through populations numerous times, killing and maiming millions of individuals. Outbreaks of influenza A H5N1 are hitting poultry and dairy farms across the nation, with impact on the economy and public health. |
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Unlock Rapid Analyses Across the Whole PDB Using BinaryCIFAs macromolecular structures available through the Protein Data Bank (PDB) archive continue to grow in complexity and size, traditional text data formats like PDBx/mmCIF and the legacy PDB file format are becoming increasingly inefficient for transfer and parsing. To support scalable data analysis, binary formats and compression techniques are now essential. Learn how to future-proof your data analysis with BinaryCIF, a fully interchangeable yet drastically more efficient flavor of the PDBx/mmCIF format. BinaryCIF not only boosts storage efficiency, but also substantially improves parsing speed, making it ideal for large-scale analyses. BinaryCIF is supported by resources such as RCSB PDB, PDBe, and AlphaFold DB. |
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Teaching Enzymology with the Protein Data Bank: From Pandemic to Paxlovid (2024)In the second edition of this webinar, SARS-CoV-2 Main Protease is used to introduce and reinforce the use of RCSB.org resources for teaching protein structure and function. |
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Understanding PDB Validation: Which experimental structures should I rely on?Learn about primary PDB structure quality metrics, including those in the validation slider graphic; how PDB structure quality varies across the archive; and identify good structure(s) for research from RCSB.org. |
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A Deep Dive into Computed Structure Model Exploration at RCSB.orgLearn how to use RCSB.org features to navigate 3D predicted protein structures in the context of experimentally-determined PDB structures. Two case studies are provided: Low-density Lipoprotein Receptor Adapter Protein 1 (LDLRAP1) and Class II aminoacyl-tRNA synthetases. |
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Visualize Biomolecular Structures with Mol*: From Atoms to MoviesMol* (MolStar) is a web application available on RCSB.org designed for visualizing biomolecular structures in 3D. |
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Teaching Enzymology with the Protein Data Bank: From Pandemic to Paxlovid (2023)This webinar uses the example of SARS-CoV-2 Main Protease to introduce or reinforce the use of RCSB.org resources for teaching protein structure and function. |
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Leveraging RCSB PDB APIs for Bioinformatics Analyses and Machine LearningThis course introduces users to the two main APIs that power the RCSB.org website: Data API and Search API. The live course consisted of two parts: Part 1 featured lectures that introduced the APIs (October 12), while Part 2 featured hands-on sessions held twice (October 19 and October 24). The hands-on session consisted of two coding examples demonstrations followed by hands-on coding in break out rooms. Only the coding demonstrations from Part 2 are available in this online course. |
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Use PDB data to their full extent: Understanding PDBx/mmCIFUnderstand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data. |
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Exploring Computed Structure Models on RCSB.orgIn August 2022, the RCSB PDB enabled access to ~1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold in addition to the ~200,000 experimentally-determined PDB structures on the RCSB.org website. A Virtual Crash Course was held to inform the RCSB.org users how to search, visualize, and analyze CSMs alongside experimentally-determined PDB structures using the custom-developed RCSB PDB tools. |
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Using KBase to access PDB Structures and Computed Structure ModelsAt this virtual course, the participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. This course was organized jointly by RCSB PDB and DOE KBase. |
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Python Scripting for Molecular Docking | Part 3In this workshop, Python scripting and libraries are used to explore ligand binding to enzymes. The corresponding Jupyter notebooks are customizable for individual research and teaching purposes. This course was developed by Paul A. Craig (Rochester Institute of Technology) and Jessica A. Nash (Molecular Sciences Software Institute). |
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Python Scripting for Biochemistry & Molecular Biology | Part 2This is the second part of the IQB Crash Course designed to introduce life scientists to the power and flexibility of solving problems with Python. This course offers a brief review of Python and the Jupyter Notebook environment first, later diving into working with Python libraries and various types of data. |
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Python Scripting for Biochemistry & Molecular Biology | Part 1This workshop familiarizes life scientists with the power and flexibility of solving problems with Python by introducing specific coding skills, as well as providing insight into the broader array of open-access resources and libraries that are available for scientific computation. This course was presented by Paul A. Craig, Professor of Biochemistry, Rochester Institute of Technology (RIT) and Jessica A. Nash, Software Scientist, Molecular Sciences Software Institute (MolSSI) |
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Boot Camp: COVID-19 Evolution and Structural BiologyThese materials were used in a June 2020 Boot Camp for undergraduate researchers held virtually to understand how the protein evolved during the first six months of the COVID-19 pandemic by exploring amino acid sequence and 3D atomic-level structure using various structural bioinformatics tools. |
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About PDB-101
Researchers around the globe make 3D structures freely available from the Protein Data Bank (PDB) archive. PDB-101 training materials help graduate students, postdoctoral scholars, and researchers use PDB data and RCSB PDB tools. Outreach content demonstrate how PDB data impact fundamental biology, biomedicine, bioengineering/biotechnology, and energy sciences in 3D by a multidisciplinary user community. Education Materials provide lessons and activities for teaching and learning.
PDB-101 is developed by the RCSB PDB.
RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.
