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

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Structure Attributes Search

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

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Sequence Similarity Search

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

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Sequence Motif Search

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

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3D Similarity Search

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

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3D Motif Search

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

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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

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Chemical Attributes

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

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Browse Annotations

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Mol* (MolStar)

3D visualization for PDB structures and ligand binding sites.

Stand-alone tool and accessible from Structure tab on Structure Summary page.

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Video Tutorials

Sequence Annotations Viewer

Graphical summaries of protein features and their relationships with UniProtKB entries

Accessible from Sequence tab on Structure Summary page

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Sequence Annotations in 3D

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

Accessible from Structure Summary page

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Genome View

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

Accessible from the Genome tab on Structure Summary page

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Pairwise Structure Alignment

Calculate pairwise structure alignments using various methods

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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

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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

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Coordinates and Experimental Data

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