Upload Structure Files to Search the PDB

New Features

Upload Structure Files to Search the PDB

04/11

Customize RCSB.org searches by uploading your own experimental data files or Computed Structure Models within seconds. This feature is particularly relevant for AlphaFold2 or ESMfold predictions, homology models, molecular dynamic trajectories, and previously unpublished structures.

In the Advanced Search Structure Similarity and Structure Motif options, use the first drop-down to switch to the “File Upload” mode and click the “Upload File” button to select a local file and upload to RCSB.org. Various file formats (.cif, .pdb, .ent) as well as gzipped (.gz) files are supported. Query results can be accessed using a unique URL for 90 days. During this time, the link can be shared and/or bookmarked, but is not accessible unless you know its exact URL.

Structure Similarity

RCSB.org uses a novel method to quickly detect similarity between protein shapes of any size.

<I>Use the first drop-down to switch to the “File Upload” mode. Use the toggle button (not shown) to include Computed Structure Models (CSMs) in the search results.</I>

Use the first drop-down to switch to the “File Upload” mode. Use the toggle button (not shown) to include Computed Structure Models (CSMs) in the search results.

Use the Advanced Search>Structure Similarity option to find proteins with similar 3D protein shapes using either a PDB ID or a URL to an external structure data file (mmCIF, BinaryCIF or PDB file format). The system attempts to assess global 3D-shape similarity by using BioZernike descriptors that capture the global volumetric shape of the protein. The search will return structures whose volumes are globally similar to the query structure provided.

Structure Motif

Structural motif similarities between PDB structures can provide valuable functional and evolutionary insights.

Use the first drop-down to switch to the “File Upload” mode. Use the toggle button (not shown) to include Computed Structure Models (CSMs) in the search results.

The Advanced Search>Structural Motif option finds structures containing a small number of specific amino acids in proximity. This feature looks for residues that appear within 15 Å of each other; the residues may be located far apart in the sequence or appear in different polymer chains.

Alternatively, use the Mol* standalone 3D viewer to interrogate a local file from your computer. You can then define a structure motif as usual and, upon submission of your query, the structure file will be automatically uploaded.