Tools for Data Exploration

Advanced Search

Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic

Structure Attributes Search

Use structural properties that have text or numerical values to build complex queries with 'AND/OR' logic

Sequence Similarity Search

Find structures that contain a similar nucleotide or protein sequence using the MMseqs2 method

Sequence Motif Search

Find structures with sequences that share small conserved regions (motifs) that have biological meaning

3D Similarity Search

Find structures that share a similar 3D shape using AI/ML-generated vector embeddings

3D Motif Search

Find structures that contain a similar 3D arrangement of residues with functional significance (catalytic or binding sites)

Chemical Search

Find small molecules by combining queries from the tools in this suite: Chemical Attributes and Chemical Similarity Search with 'AND' logic

Chemical Similarity

Search for small molecules using SMILES, InChI, or chemical formula

Chemical Attributes

Combine chemical properties that have text or numerical values with AND/OR logic

Browse Annotations

Find PDB structures using annotations from various ontologies and hierarchical classification schemes, e.g. Disease Ontology, Molecular Function

New Entries

Search entries released since last archive update on Tuesday

Unreleased Entries

Search entries that are being processed, on hold waiting for release, or have been withdrawn

PDB Statistics

PDB data distribution, archive growth, and more

Mol* (MolStar)

3D visualization for PDB structures and ligand binding sites.

Sequence Annotations Viewer

Graphical summaries of protein features and their relationships with UniProtKB entries

Sequence Annotations in 3D

Map protein sequence features onto the 3D structure of protein assemblies

Genome View

Explore the correspondences between PDB entity sequences, genes, and genomes

Pairwise Structure Alignment

Calculate pairwise structure alignments using various methods

Symmetry Resources in the PDB

Explore tools that display global, local, and helical symmetry among subunits

Structure Quality

From 3D views, through graphical sliders, charts, and color codes, the resources to determine the quality of PDB Structures, ligands, and Computed Structure Models are accessible throughout the RCSB.org website

Grouping Structures

Grouping structural data helps gather information about and explore multiple structures at a level higher than an individual structure

PDB Statistics

PDB data distribution, archive growth, and more

PDB Citation MeSH Network Explorer

Find connections between articles describing PDB structures using MeSH terms

EPPIC Biological Assemblies

EPPIC (Evolutionary Protein-Protein Interface Classifier) finds biological interfaces from crystal contacts

External Data and Resources

External resources are indicated in orange on RCSB.org

• Integrated Resources

• Additional Resources

Coordinates and Experimental Data

Enter PDB IDs to download multiple files in batches containing one or more file formats

Sequences

Enter PDB IDs to download sequences in FASTA format

Ligands

Enter the chemical component IDs to download SDF files with ligand coordinates

File Download Services

Download PDB archive or other related data files

Web APIs

Several APIs power the RCSB.org website and are open to the community for programmatic access