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The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond.
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SARS-CoV-2 Spike Variants
Deposition Preparation Tools
Data Extraction
pdb_extract: Extract and harvest data in PDBx/mmCIF format from structure determination programs
SF-Tool: Convert structure factor files among various formats
Small Molecules
Ligand Expo: Search the Chemical Component Dictionary for the IDs of released ligands
Data Format Conversion
PDBML2CIF: Convert PDBML-format data into PDBx/mmCIF-format
PointSuite: Generate symmetry records for macromolecular assemblies with point and helical symmetries
MAXIT: Translate data between file formats and more
Validation Services
Validation reports contain an assessment of the quality of a structure and highlight specific concerns by considering the coordinates of the model, the experimental data and the fit between the two. Easily interpretable summary information that compares the quality of a model with that of other models in the archive will help users of PDB data to critically assess archived entries and to select the most appropriate structural models for their needs. These reports are developed using the recommendations of thewwPDB Validation Task Forces.
Reports for released entries are available from Structure Summary pages.
Validation reports for manuscript reviewers are created during annotation of deposited structures.
Have non-atomic coordinates, multi-scale structures obtained through integrative/hybrid (I/H) methods? Deposit at PDB-Dev which is a prototype deposition and archiving system for structural models obtained through integrative/hybrid (I/H) methods.
From any page on the site, a Basic Search can be run by entering a search term in the top Search Bar.
As you enter a term, you will see suggestions appearing in the dropdown menu that appears below the search bar. The suggestions are grouped by attribute name, indicating in the specific field or fields in which the search term was found.
You can click on an item in the dropdown menu to see results matching only that particular attribute, or click the
Search icon to see results matching multiple fields.
Advanced Search
The Advanced Search Query Builder tool allows you to construct complex boolean queries by specifying values for a wide range of structure attributes.
Text-based queries can be combined with sequence and structure similarity searches.
Search results can be returned at the structure, entity, or assembly level, and viewed in a variety of formats, for example, as a summary view, an images only gallery view, or in a Tabular Report format.
Any query and its results can be further refined by selecting additional criteria from the 'Refinements' panel.
Search protein and nucleic acid sequences using the mmseqs2 method to find similar protein or nucleic acid chains in the PDB.
The new Advanced Search Query Builder tool can be used to run sequence searches, and to combine the results with the other search criteria that are available.
You can search the PDB archive for a specific ligand or similar ligands based on the 2D chemical drawing of a molecule. In doing so you don’t have to know the specific chemical descriptors (e.g., SMILES and/or InChI) because they will be automatically generated. You can also edit a molecule that is drawn or loaded into the tool to add or remove atoms or groups of atoms and then use the new molecule to query the PDB archive.
Phase I: Every Saturday by 3:00 UTC, for every new entry, wwPDB website provides sequence(s) (amino acid or nucleotide) for each distinct polymer and, where appropriate, the InChI string(s) for each distinct ligand and the crystallization pH value(s).
Phase II: Every Wednesday by 00:00 UTC, all new and modified data entries will be updated at each of the wwPDB FTP sites.
Drugs & Drug Targets in the PDB have been mapped to DrugBank. They have been made available through the integrated search system. You can find some search examples under the help examples page.
Drug-Target Complex: Atorvastatin bound to its target HMG-CoA reductase
Provides a graphical summary of biological and structural protein features of PDB entities and how they correspond to UniProtKB sequences. It loads features from RCSB PDB webservices and third party resources such as UniProtKB, CATH or SCOPe.
This feature is available in Structure Summary pages and Instance Sequence pages.
Genome View
Illustrates the correspondences between PDB Entity sequences and genomes.
When the relationships between PDB Entities and genes are available, PDB Entity sequences are mapped to their genome positions
to show which regions of a gene are available in the Entity coordinates.
This feature is available from the Structure Summary page Genome tab.
Pairwise Structure Alignment
The protein structure alignment tool allows for calculating pairwise structure alignments using different alignment methods.
See the detailed documentation at this help page. Comparisons can be made for
any protein in the PDB archive and for customized or local files not in the PDB.
Also, the standalone Mol* viewer application allows for calculating pairwise structure alignments based on sequence alignment. See
detailed instructions on how to superpose structures at the Mol* help page.
Protein Symmetry
The Mol* symmetry display mode (select the Assembly Symmetry button) highlights global, local, and helical symmetry among subunits. The view displays the symmetry axes, a polyhedron that reflects the symmetry, and a color scheme that emphasizes the symmetry.
Structure Summary pages provide access to information about structure quality.
The slider graphic compares important global quality indicators for a given structure with the PDB archive. Global percentile ranks (black vertical boxes) are calculated with respect to all X-ray structures available prior to 2011. Resolution-specific percentile ranks (white vertical boxes) are calculated considering entries with similar resolution.
This graphic is from the wwPDBValidation Report , which provides a more detailed assessment of the quality of a structure and highlights specific concerns. These reports were created using the recommendations of wwPDB Validation Task Forces.The full wwPDB Validation Report PDF is available for download. PDFs of Ramachandran plots (created by MolProbity) are provided to offer an independent method to evaluate the conformational quality of protein structures.
For examples, view the Structure Summary pages for 1CBS (1.8Å structure of a small protein and a ligand , an entry with better overall quality relative to all X-ray structures) and 1FCC (a 3.2Å structure with worse overall quality relative to all X-ray structures).
Map Genomic Locations to/from PDB
The 1D-coordinates API provides means to map between genomic coordinates and PDB positions. Find more information about this and other APIs in the webservices page.
EPPIC (Evolutionary Protein-Protein Interface Classifier) provides value-added information about biological assemblies in the PDB. This web server classifies interfaces present in protein crystals to distinguish biological interfaces from crystal contacts. EPPIC Version 3 enumerates all possible symmetric assemblies with a prediction of the most likely assembly based on probabilistic scores from pairwise evolutionary scoring.
The National Library of Medicine assigns MeSH (Medical Subject Headings) from a controlled vocabulary to index articles for PubMed. MeSH terms typically appear in a hierarchical tree structure that starts with 16 main branches. The PDB Citation MeSH Network Explorer flattens these trees into co-occurence networks of MeSH terms associated with PDB entries. Each node on the graph is a publication, and nodes are linked when they share MeSH terms.
Download Coordinate & Experimental Data Files
By entering PDB IDs, multiple files can be downloaded in batches containg one or more file formats.
Coordinate Data Files can be downloaded in the following formats:
PDB
PDBx/mmCIF
PDBML/XML
PDBML/XML (Header only)
Biological Assemblies in PDB
Biological Assemblies in PDBx/mmCIF
Experimental Data Files can be downloaded in the following formats:
Searches and reports performed on this RCSB PDB website utilize data from the PDB archive. The PDB archive is maintained by the wwPDB at the main archive, ftp.wwpdb.org (data download details) and the versioned archive, ftp-versioned.wwpdb.org (Versioning details).
Major Directories
The directory pub/pdb is the entry directory for the PDB archive.
The directory pub/pdb/data/structures/divided contains the current PDB contents including PDB, mmCIF, and PDBML/XML formatted coordinate files, structure factors and NMR restraints
John D. Westbrook Jr. (1957-2021) passed away on October 18, 2021. He was incredibly beloved and respected by his colleagues at Rutgers and throughout the world, known for his dry wit and endless enthusiasm for thinking about all aspects of data and data management.
PDB50; Opioids and Pain Signaling Video; Explore Ligand Quality; User Survey; and more; Education Corner on The SARS-CoV-2 Virion: Magnifying the Miniscule with Models of Digital, Plastic, and Paper. Fall 2021 Issue
Download the 2020 Annual Report (PDF) for an overview of activities relating to Deposition/Biocuration, Archive Management/Access, Data Exploration, and Outreach/Education.
