Data Exploration Services

Recently-introduced Search and Data APIs offer comprehensive functionality and high performance.

The new Search API allows users to run queries across RCSB PDB Search Services and retrieve a list of relevant identifiers such as PDB IDs, entity IDs, assembly IDs, and more.

Documentation is available to help users learn the concepts and syntax behind the new services. Use this documentation to display all of the details of a specific API request, and then run the search request and to see the response.

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Use the Advanced Search>Sequence option to search protein, DNA, or RNA sequences using mmseqs2 software. A description of this functionality is available.

Zoom using the mouse scroll (wheel) or the mousepad/touchpad to show the amino acid sequence and mismatches. Help documentation is available.

Advanced Search Query Builder can be used combine these Sequence Searches with other types of searches using Boolean operators (AND/OR/NOT):

1. Attribute searching: specific fields or full-text search across all fields, such as ID, deposition information, entry features, and experimental information
2. Sequence searching: based on a FASTA sequence (with E-value or % Identity cutoffs);
3. Sequence Motif searching: find short sequence patterns in PDB structure FASTA sequences using Simple, PROSITE, or RegEx syntax
4. Structure Similarity searching: based on an existing Chain or Assembly of a PDB structure
5. Chemical Search: find chemical components by Formula or descriptor

Use Advanced Search>Attribute Search to query specific fields in the database or to perform a full-text query across all fields.

The database maintains a long list of attribute fields. Users can browse the pull-down menu of options, or search to find relevant categories. For example, type resolution to find the corresponding database attributes that can be queried.

Entering the word resolution highlights the related attributes that can be searched.

A new data representation for carbohydrates in PDB entries and reference data improves the Findability and Interoperability of these molecules in macromolecular structures.

Access oligosaccharide Information from Structure Summary pages (example: 1b5f), including names, 2D Symbol Nomenclature For Glycans (SNFG) images, glycosylation sites, and 3D interaction view. BIRD molecules for entries containing commonly-known di-, tri- saccharides or blood antigens that have BIRD definitions are also listed.

Structure Summary page focused on oligosaccharide Information

The Mol* 3D view options displays 3D SNFG representations for carbohydrates for easy identification of sugars and their neighboring environment.

Mol* 3D view with oligosaccharides shown using same color scheme as 2D SNFG diagram

From the top bar Basic Search, find oligosaccharide containing entries by a specific glycosylation site or by an exact linear descriptor provided in the PDB files.

Use Advanced Search to find entries with glycosylation in the Polymer Molecular Features or entries with Oligosaccharide Features by searching any of these attributes: linear descriptors, systematic name, monosaccharide composition, etc.

Advanced Search options

Oligosaccharide features from the return of search results can be created and downloaded using pre-defined Oligosaccharide or Custom tabular report.

Items in the Oligosaccharide Report can also be used to generate a Custom Report