Data Exploration Services

RCSB PDB has recently introduced DNS names for programmatic access to PDB archive downloads:

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The File Download Services documentation has detailed information.

Starting September 2023, RCSB PDB will start enforcing use of these updated DNS names. URLs in which the DNS name doesn’t match the protocol (e.g., https://ftp.rcsb.org, ftp://files.rcsb.org) will no longer work at that time.

Users who download PDB archive data programmatically are encouraged to switch to the new DNS names as soon as possible. HTTPS protocol is preferred (over FTP) for individual file downloads.

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Mol* view of PDB structure1dtj. To select this coloring scheme, select the “Experimental Support Confidence” option under Quality Assessment.

A new Mol* 3D option displays PDB structures determined with X-ray crystallography using a coloring scheme similar to what is used to show Computed Structure Models confidence levels. This feature is available for most crystal structures in the PDB with structure factors.

This display option was developed using individual-residue Real Space Correlation Coefficient (RSCC) values that indicate how well the atomic coordinates for an individual residue are supported by X-ray crystallographic experimental data. Individual RSCC values vary with both residue chemical structure and structure resolution. Therefore, the RSCC values for each type of amino acid in PDB X-ray structures at different resolutions were ranked from lowest to highest, indicating worse to better experimental data support for residue atomic coordinates.

Amino acid residues in any PDB structure are colored by their RSCC value ordinal ranking:

• Blue (25-100%): very well resolved residues, very high confidence
• Cyan (5-25%): well resolved residues, high confidence
• Yellow (1-5%): outlier residues, low confidence
• Orange (<1%): extreme outlier residues, very low confidence

With the RSCC-based confidence score and color scheme, RSCC outliers are readily apparent in ribbon representation 3D graphical displays, in a color scheme consistent with the pLDDT (predicted lDDT-Cα)-based confidence coloring scheme used for Computed Structure Models.

For a description of how the quality measures were developed, see
Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level, Structure (2022) doi: 10.1016/j.str.2022.08.004

This study also demonstrates that while RSCC values in a crystal structure are correlated with pLDDT scores in the corresponding AlphaFold2 model, crystal structures in the PDB are generally more reliable than AlphaFold2 models.

Mol* also supports a coloring scheme based on wwPDB Validation Reports that indicates the number of geometry related problems for a specific residue (e.g., geometry outliers, and clashes).

A new Mol* 3D option displays PDB structures determined with X-ray crystallography using a coloring scheme similar to what is used to show Computed Structure Models confidence levels. This feature is available for most crystal structures in the PDB with structure factors.

This display option was developed using individual-residue Real Space Correlation Coefficient (RSCC) values that indicate how well the atomic coordinates for an individual residue are supported by X-ray crystallographic experimental data. Individual RSCC values vary with both residue chemical structure and structure resolution. Therefore, the RSCC values for each type of amino acid in PDB X-ray structures at different resolutions were ranked from lowest to highest, indicating worse to better experimental data support for residue atomic coordinates.
Amino acid residues in any PDB structure are colored by their RSCC value ordinal ranking:

• Blue (25-100%): very well resolved residues, very high confidence
• Cyan (5-25%): well resolved residues, high confidence
• Yellow (1-5%): outlier residues, low confidence
• Orange (<1%): extreme outlier residues, very low confidence

With the RSCC-based confidence score and color scheme, RSCC outliers are readily apparent in ribbon representation 3D graphical displays, in a color scheme consistent with the pLDDT (predicted lDDT-Cα)-based confidence coloring scheme used for Computed Structure Models.

For a description of how the quality measures were developed, see

Assessing PDB macromolecular crystal structure confidence at the individual amino acid residue level, Structure (2022) doi: 10.1016/j.str.2022.08.004

Use the Chemical Sketch Tool to draw or edit a molecule, then use the resulting SMILES or InChI string to search for matching molecular definitions in the PDB Chemical Component Dictionary.

This tool uses the web-based chemical drawing tool Marvin JS from ChemAxon to compose chemical sketches for chemical similar and substructure searches. Documentation is available.

Access the Chemical Sketch Tool from the top Search menu or from Advanced Search in the Chemical Search options.

Basic Sequence Search. Use the slider button to include Computer Structure Models in the Search Results.

Enter a sequence in the top search bar to search for matching PDB entities.

Sequence Searches at RCSB.org use MMseqs2 to find similar protein and nucleic acid sequences in the archive.

For example, a search for the sequence FVNQHLCGSHLVEALYLVCGERGFFYTPKT will currently return >400 entities for exploration. Including the option for CSMs will add ~100 more examples.

Search Results including PDB experimental structures and CSMs. A) Use the Refinements panel on the left to limit the results based on characteristics including Structure Determination Method and Source Organism. B) Results can be sorted using the pulldown feature on the right.

References

• RCSB.org Sequence Documentation
• MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets (2017) Nat Biotechnol 35: 1026–1028 doi: 10.1038/nbt.3988

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