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As 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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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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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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Learn 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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Mol* (MolStar) is a web application available on RCSB.org designed for visualizing biomolecular structures in 3D.
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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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This 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 Otober 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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Understand 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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In 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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At 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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In 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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This 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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This 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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These 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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