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RCSB PDB Training Events: April 2025 Office Hour: Depositing IHM Data to the PDB Archive

Monday, April 7, 2025 from 1pm -2:00pm Eastern | 10:00am - 11am Pacific

PDB-IHM has been unified with the PDB to deliver integrative structures alongside experimental structures in the PDB archive [https://files.wwpdb.org/pub/]. Integrative structures can be deposited through the PDB-IHM deposition portal [https://data.pdb-ihm.org/] and accessible from the wwPDB OneDep home page [https://deposit.wwpdb.org/]. They are assigned PDB IDs and DOIs, and can be accessed from the PDB archive, PDB DOIs, and the PDB-IHM website [https://pdb-ihm.org/].

Interested in learning more about the deposition, validation, and biocuration of structures determined using integrative and hybrid methods (IHM) in the PDB archive? Bring your questions to a virtual office hour.

Participation is free, but registration is required. [https://go.rutgers.edu/26rmmnub]

Office Hour: Sequence Annotations Viewer

Thursday, April 7, 2025 from noon-1:00pm Eastern | 9:00am - 10am Pacific

The Sequence Annotations Viewer [https://www.rcsb.org/docs/sequence-viewers/sequence-annotations-viewer] provides graphical summaries of PDB protein biological and structural features and their relationships with UniProtKB entries.

Structural features such as secondary structure, angle/distance outliers, protein-ligand binding sites or disulfide bridges, are extracted from the PDB structural data. Additionally, structural domains are annotated from CATH and SCOPe databases. Biochemical and biomedical features are collected from the UniProtKB database and mapped onto PDB sequences.

Participation is free, but registration is required. [https://go.rutgers.edu/exi9io2q]

Crash Course:

Python For Cheminformatics-Driven Molecular Docking

Thursday, May 1, 2025, from 1-5pm Eastern, 10am-2pm Pacific

In this workshop, we will use Python scripting to explore and compare small molecules that bind to the SARS-CoV2 main protease. We will be working in a Google CoLab environment and will use a number of libraries that are heavily used for cheminformatics.

At the completion of this workshop, users will be able to:

Search BindingDB and create molecular datasets.Use RDKit to manipulate and process molecules.Compare features of families of small molecules using plots and fingerprint analysisCreate a workflow for docking multiple ligands to the main protease

Participation is free, but registration is required. [https://go.rutgers.edu/gkgpqrih]

PDB-101: Exploring Structural Biology with CSMs

Want to learn more about Computed Structure Models from AI/ML?

The Guide to Understanding PDB Data includes an introduction to Computed Structure Models [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/computed-struc...] that provides background on Using Computed Structure Models and a Case Study of the Computed Structure Model of the Src Oncoprotein.

[https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/computed-struc...]

The crystallographic structure of the inactive conformation (left, PDB ID 2src [https://www.rcsb.org/structure/2SRC]) and the Computed Structure Model of human Src oncogene protein predicted by AlphaFold2 (RCSB.org assigned ID AF_AFP12931F1 [https://www.rcsb.org/structure/AF_AFP12931F1], right). Visit PDB-101 for details [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/computed-struc...].

PDB-101 training materials, such as the Guide to Understanding PDB Data [https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction] and webinars [https://pdb101.rcsb.org/train/training-events], are available to help graduate students, postdoctoral scholars, and researchers use PDB data and RCSB PDB tools. Recordings of past webinars are also available [https://pdb101.rcsb.org/train/training-events]. Visit PDB-101 [https://pdb101.rcsb.org] for more.

RCSB Protein Data Bank is managed by Rutgers, The State University of New Jersey; University of California, San Diego/San Diego Supercomputer Center; and University of California San Francisco.

RCSB PDB Core Operations are funded by the National Science Foundation [http://www.nsf.gov/] (DBI-2321666), the US Department of Energy [http://science.energy.gov/] (DE-SC0019749), and the National Cancer Institute [http://www.cancer.gov/], National Institute of Allergy and Infectious Diseases [http://www.niaid.nih.gov/], and National Institute of General Medical Sciences [http://www.nigms.nih.gov/] of the National Institutes of Health [http://www.nih.gov/] under grant R01GM157729.

[http://rcsb.org]

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