Data Exploration Services

Use Advanced Search to find short sequence patterns in PDB structure FASTA sequences using the following syntax options:

1. Simple: Sequence fragments using IUPAC one-letter codes for amino acids (e.g., MQTIF) plus ‘X’ to indicate any amino acid at a position. For example, use XPPXP to search for SH3 domains (where X is a variable residue and P is Proline)
2. PROSITE: Complex queries that include ambiguities, exempt amino acids, repetition, and/or positioning at N- or C-terminus can be expressed using PROSITE patterns (e.g., [AC]-x-V-x(4)-{ED}).Visit PROSITE for definitions
3. Regex: Build complex sequence searches using regular expressions (Details)

Set "Display Results as" to Polymer Entities to view the numbering for the sequential sequence match region (corresponding to PDBx/mmCIF file numbering).

Recent improvements to RCSB.org include revised and updated tools for searching and exploring PDB data.  As a result, select RCSB PDB Services are being replaced or retired.

New: MyPDB Service

To utilize the new and improved MyPDB features, users should generate a new MyPDB account using third-party authentication (Google, Facebook, or ORCID).

Legacy MyPDB users are encouraged to generate new MyPDB accounts. Legacy email notifications will continue to be sent until approximately October 2020. Users are encouraged to use these alerts to update the settings in their new accounts.

Retiring: Legacy RCSB PDB APIs

Recently-introduced Search and Data APIs offer comprehensive functionality and high performance. As a result, legacy RCSB PDB APIs (REST search and fetch) will be discontinued in November 2020.
Additionally, the new APIs will enable access to the remediated carbohydrate data that will be released in July. Legacy APIs will not support these data.

Users of the legacy APIs are strongly encouraged to migrate to the new APIs before November 2020. Please contact us with any questions about the new and improved APIs.

Retired: REST Services Replaced By New APIs

REST.rcsb.org services were deprecated in May. These services have been replaced by more powerful and comprehensive APIs that drive the new and improved RCSB.org.

Retired: Protein Workshop and Ligand Explorer

Java-based tools Protein Workshop and Ligand Explorer were retired in June. The 3D viewer Mol* has been updated to include features from these tools..

Mol* includes features such as viewing ligand environments; measuring distances within a structure; highlighting particular structural regions using the sequence display; changing the representation of particular residues; displaying symmetry related molecules; and displaying electron density maps.

A new and improved PDB-Dev website is now available. PDB-Dev is a prototype system which helps wwPDB partners to understand the requirements in archiving integrative structures. It has been built based on recommendations from the wwPDB Integrative/Hybrid Methods (I/HM) Task Force. PDB-Dev currently consists of 37 integrative structures of macromolecular complexes.
The updated PDB-Dev web interface provides dynamic and responsive web pages and includes two new features:

• A new search service that facilitates the retrieval of structures archived in PDB-Dev. The current implementation supports search by macromolecular names, entry identifiers, experimental data types, author names, citations, software and several other keywords.
• Complex queries with Boolean operators and wildcards are supported. Search results can be downloaded as csv or Excel files.

The PDB-Dev team welcomes feedback from users. Please send comments and suggestions to pdb-dev@mail.wwpdb.org.