Searching the PDB for High-Quality Ligand-Bound Structures
Webinar hosted by RCSB PDB and Rutgers Institute for Quantitative Biomedicine | September 8, 2025
High-quality ligand-bound structures are indispensable for understanding the interaction between small molecule ligands and their target proteins and nucleic acids. In this webinar, we illustrate the PDB ligand validation and annotation process, and explain the metrics that measure ligand quality from various perspectives. Learn how to search the PDB for high-quality ligand-bound structures using these metrics via RCSB.org and RCSB PDB APIs.
Course Objectives and Intended Audiences
After watching the videos in this course, you will be able to:
- Understand PDB ligand validation process and ligand quality metrics
- Use the metrics to assess the quality of a particular ligand structure
- Compare multiple structures of the same ligand in different PDB entries
- Search PDB for best examples of ligands using text, chemical drawing, and APIs
This course is intended for:
- Graduate students and postdoctoral researchers in biomedical science
- Faculty members and professionals involved in ligand-macromolecule interaction study and drug design
- Undergraduate students in any biology and/or biochemistry discipline
Course Videos
Click on the image below to play the video.
Introduction
Chenghua Shao, Ph.D.
Scientific Software Developer, RCSB PDB/Rutgers
Ligand Data in the PDB
Chenghua Shao, Ph.D.
Ligand Validation at the PDB
Chenghua Shao, Ph.D.
Ligand Quality Comparison within the PDB
Chenghua Shao, Ph.D.
Demonstration: Searching for ligands of better quality using RCSB.org and RCSB PDB APIs
Chenghua Shao, Ph.D.
