Searching and Downloading Small Molecules in the PDB
Webinar hosted by RCSB PDB | February 26, 2026
Join Dr. Alison Biester to learn about robust resources offered by RCSB PDB and wwPDB for accessing chemical and structural information about small molecules within the structure entries of the Protein Data Bank.
Course Objectives and Intended Audiences
After watching the videos in this course, you will be able to:
- Use the re-organized RCSB PDB Chemical Search tools to screen small molecules for structural similarity to a query chemical molecule or to search by attribute such as chemical names, synonyms, SMILES, InChI, and InChiKey
- Use the RCSB PDB Search and Data APIs to programmatically obtain small-molecule components of interest
- Download data for all small molecules in the PDB, including the full wwPDB Chemical Component Dictionary (CCD) or descriptors such as SMILES, InChI, or InChIKey files from the wwPDB CCD resources
- Understand PDB ligand validation process and how to choose high quality ligand structures
This course is intended for:
- Graduate students and postdoctoral scholars in biomedical sciences
- Faculty members and professionals involved in ligand-macromolecule interaction study and drug design
- Undergraduate students in any biology and/or biochemistry discipline
Additional Resources
Course Videos
Click on the image below to play the video.
Welcome and Agenda
Alison Biester, Ph.D.
Scientific Researcher, RCSB PDB
Introduction to PDB and Chemical Component Dictionary (CCD)
Alison Biester, Ph.D.
Using RCSB PDB Chemical Search Tools
Yana Rose, Ph.D.
Using RCSB PDB Search and Data APIs
Alison Biester, Ph.D.
PDB Ligand Validation
Alison Biester, Ph.D.
Downloading CCD Data
Alison Biester, Ph.D.
Demonstration
Alison Biester, Ph.D.
Conclusions and Closing
Alison Biester, Ph.D.
