Uploaded March 2026 | Updated September 2026, 3 weeks ago
The RCSB PDB Advanced Search tool allows users to build precise and complex queries of the PDB archive. Learn how to build complex queries, including 3D structural searches that are integrated with interactive Mol* visualization and how to use the Chemical Search option.
After watching this video, you will be able to:
• Determine the best search tool or tools to identify structures of interest
• Select an attribute for searching (e.g., Organism, Experimental Method, Resolution) and add conditions to narrow results
• Find structures that contain a similar nucleotide or protein sequence
• Find structures with sequences that share small conserved regions (motifs) that have biological meaning
• Find structures that share a similar 3D shape
• Find structures that contain a similar 3D arrangement of residues with functional significance (catalytic or binding sites)
• Search and explore experimental structures, integrative structures, and Computed Structure Models (CSMs)
Video chapters:
00:00 Introduction: Protein Data Bank and RCSB PDB
01:55 Advanced Search For 3D Structure Discovery
03:41 Overview of Advanced Search Tools on RCSB.org
07:30 Accessing the Advanced Search
07:50 Introduction to Structure Attributes Search
09:27 Introduction to Sequence Similarity Search
12:35 Introduction to Sequence Motif Search
14:04 Introduction to 3D Similarity Search
16:50 Introduction to 3D Motif Search
24:00 Case Study: Trypsin Catalytic Site
26:33 Search Results Exploration
34:07 Chemical Search Capabilities
Additional resources for this webinar are available on pdb101.rcsb.org/train/training-events/advanced-search
Explore all training courses at pdb101.rcsb.org/train/training-events
The RCSB PDB Advanced Search tool allows users to build precise and complex queries of the PDB archive. Learn how to build complex queries, including 3D structural searches that are integrated with interactive Mol* visualization and how to use the Chemical Search option.
After watching this video, you will be able to:
• Determine the best search tool or tools to identify structures of interest
• Select an attribute for searching (e.g., Organism, Experimental Method, Resolution) and add conditions to narrow results
• Find structures that contain a similar nucleotide or protein sequence
• Find structures with sequences that share small conserved regions (motifs) that have biological meaning
• Find structures that share a similar 3D shape
• Find structures that contain a similar 3D arrangement of residues with functional significance (catalytic or binding sites)
• Search and explore experimental structures, integrative structures, and Computed Structure Models (CSMs)
Video chapters:
00:00 Introduction: Protein Data Bank and RCSB PDB
01:55 Advanced Search For 3D Structure Discovery
03:41 Overview of Advanced Search Tools on RCSB.org
07:30 Accessing the Advanced Search
07:50 Introduction to Structure Attributes Search
09:27 Introduction to Sequence Similarity Search
12:35 Introduction to Sequence Motif Search
14:04 Introduction to 3D Similarity Search
16:50 Introduction to 3D Motif Search
24:00 Case Study: Trypsin Catalytic Site
26:33 Search Results Exploration
34:07 Chemical Search Capabilities
Additional resources for this webinar are available on pdb101.rcsb.org/train/training-events/advanced-search
Explore all training courses at pdb101.rcsb.org/train/training-events
