PDB Search & Download on the platform

PDB Search and Download retrieve experimentally determined 3D structures — solved by X-ray crystallography, cryo-EM, or NMR — from the RCSB Protein Data Bank. Reach for it when an experimental structure exists, especially one with a co-crystallized ligand: it is the highest-confidence structure you can get. If no experimental structure has been deposited, predict one instead — fetch a known protein with AlphaFold or fold a novel sequence with ESMFold. See what you can achieve for the full set.

What PDB Search does

PDB Search queries the RCSB Protein Data Bank (PDB), the global archive for experimentally determined three-dimensional structures of biological macromolecules, growing by tens of thousands of new depositions each year through X-ray crystallography, cryo-electron microscopy (cryo-EM), NMR spectroscopy, and other methods. On the platform, PDB Search and PDB Download run when you ask Ivy in chat (there is no form or job for them); they call RCSB directly on CPU with no GPU requirements, returning results in 3-30 seconds.

The RCSB PDB is managed by the Research Collaboratory for Structural Bioinformatics and is the U.S. data center of the Worldwide Protein Data Bank (wwPDB). Every experimentally determined macromolecular structure published in a scientific journal is required to be deposited in the PDB.

Citations

Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Research. 2000;28(1):235-242. doi: 10.1093/nar/28.1.235

Burley SK, Bhikadiya C, Bi C, Bittrich S, Chao H, Chen L, et al. RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. Nucleic Acids Research. 2023;51(D1):D488-D508. doi: 10.1093/nar/gkac1077

Key capabilities

• Full-text search: Find structures by protein name, organism, author, ligand name, or any keyword
• Structure download: Retrieve PDB or mmCIF format files by PDB ID
• Metadata retrieval: Get resolution, experimental method, organism, release date, chain information, and bound ligands
• Resolution-based filtering: Focus on high-resolution structures suitable for detailed analysis
• Direct chaining: Downloaded structures feed immediately into DiffDock, P2Rank, PDB2PQR, and MM-GBSA

How it works technically

The platform runs two PDB operations, each wrapping a different RCSB API. Both run when you ask Ivy in chat:

PDB Search

Uses the RCSB Search API v2 to find structures matching a text query. The search process:

1. Query submission: The platform sends a full-text search query to https://search.rcsb.org/rcsbsearch/v2/query as a POST request with the query string.
2. ID retrieval: The API returns matching PDB IDs ranked by relevance, along with a total count.
3. Metadata enrichment: For the top 10 results, the platform fetches detailed metadata from the RCSB Data API (https://data.rcsb.org/rest/v1/core/entry/{pdbId}), extracting title, experimental method, resolution, organism, and release date.

PDB Download

Downloads the actual structure file content from https://files.rcsb.org/download/{pdbId}.{format}. Supports PDB and mmCIF (CIF) formats.

When to use PDB Search

Primary use cases

Structure-based drug design

• Find high-resolution crystal structures of drug targets with bound ligands
• Identify co-crystal structures showing how existing drugs bind to a target
• Source structures for molecular docking with DiffDock
• Select the best available structure for binding site analysis with P2Rank

Protein structure analysis

• Retrieve experimental structures to compare with AI predictions (ESMFold, AlphaFold)
• Examine protein-protein interaction interfaces
• Analyze domain organization and quaternary structure
• Study conformational changes across different crystal forms

Target validation

• Confirm that structural data exists for a potential drug target
• Assess structural quality (resolution, completeness) for downstream computational work
• Identify available structures with different ligands or mutations
• Map binding sites and allosteric pockets

Cryo-EM structure retrieval

• Find large macromolecular complex structures determined by cryo-EM
• Retrieve viral spike proteins, ribosomes, and membrane protein complexes
• Access structures at resolutions increasingly comparable to X-ray crystallography

PDB Search vs. AlphaFold vs. ESMFold

Rule of thumb: Use PDB when an experimental structure exists (especially with bound ligands). Use AlphaFold Fetch for quick access to predicted structures for well-known proteins. Use ESMFold when no existing structure is available.

When to use alternatives

Integration with the platform ecosystem

Upstream data sources

PDB Search accepts input from:

• Free-text chat queries: Protein names, PDB IDs, or descriptive searches
• UniProt results: PDB cross-references from UniProt entries
• BLAST results: Homologous structures identified by sequence similarity
• Entrez Search: Structure records from NCBI's structure database

Downstream applications

PDB structures feed into:

• DiffDock: Molecular docking using the experimental structure as the protein target
• P2Rank: Binding site prediction on the 3D structure
• PDB2PQR: Electrostatic calculations and protonation state assignment
• MM-GBSA: Binding free energy rescoring for docked poses
• Mol viewer*: Interactive 3D visualization on the canvas

Workflow chaining examples

Structure-to-docking pipeline:

1. PDB Search for "EGFR kinase high resolution"
2. PDB Download for the best structure (e.g., 1M17)
3. DiffDock for molecular docking with a candidate ligand
4. MM-GBSA for complex minimization and an energy report (not a binding affinity)

Target characterization pipeline:

1. UniProt Search for protein annotations
2. PDB Search for experimental structures (via cross-references)
3. P2Rank for binding site prediction
4. DiffDock for ligand docking

Scope and limitations

Coverage

• Total structures: growing continuously; check RCSB PDB statistics for the current count
• Growth rate: tens of thousands of new structures deposited per year
• Methods: X-ray crystallography (~85%), cryo-EM (~12%), NMR (~2%), other (~1%)
• Organisms: Structures from thousands of organisms, with human and common model organisms best represented

Limitations

• Coverage gaps: Not all proteins have experimental structures. The PDB covers a fraction of the known protein universe. For proteins without PDB entries, use ESMFold or AlphaFold Fetch.
• Resolution variability: Structure quality varies widely. Some entries have excellent resolution (<1.5 A) while others are low resolution (>4.0 A). Always check resolution before using a structure for detailed analysis.
• Static snapshots: Crystal structures represent a single conformational state. Proteins in solution may adopt different conformations relevant to drug binding.
• Crystal packing artifacts: Some structural features may be influenced by crystal contacts rather than biological interactions.
• Metadata search only: PDB Search performs full-text search. Structured queries (by resolution range, method, ligand presence, etc.) are not supported; ask Ivy to filter the returned hits by the resolution and method that come back with each one.
• Top 10 enrichment: For performance, metadata is fetched for only the top 10 search results. Additional PDB IDs are listed without detailed metadata.

Performance characteristics

• Search runtime: 3-10 seconds for text search, plus 1-2 seconds per entry for metadata enrichment
• Download runtime: 2-5 seconds for structure file retrieval
• Maximum search results: Up to 100 PDB IDs returned, with full metadata for the top 10
• File sizes: PDB files typically range from 100 KB to 10 MB depending on structure size

References

• RCSB PDB: https://www.rcsb.org/
• RCSB Search API documentation: https://search.rcsb.org/
• RCSB Data API documentation: https://data.rcsb.org/
• Berman HM et al. The Protein Data Bank. Nucleic Acids Res. 2000;28(1):235-242. doi: 10.1093/nar/28.1.235

Chat Usage

Example Prompts

• "Download EGFR kinase structure 1M17 from PDB"
• "Search PDB for BRAF kinase structures with resolution below 2.0"
• "Find cryo-EM structures of the SARS-CoV-2 spike protein"

Workflow Chaining

• Feeds into: DiffDock (docking), P2Rank (pocket prediction), PDB2PQR (electrostatics), MM-GBSA (rescoring)
• Accepts from: UniProt (cross-referenced PDB entries), BLAST (homologous structures)

FAQ

Read next