Search Related Features

Basic Search

From any page on the site, a Basic Search can be run by entering a search term in the top Search Bar.

Use the dropdown to the left of the search bar to define the search scope, which can be either “PDB Archive” or “Documentation”.

As you enter a term, you will see a list suggestions in the dropdown menu that appears below the search bar. You can click on an item in the menu, or, if no menu appears for the term or terms you have entered, click the
Search icon. If “PDB Archive“ is selected, suggestions are grouped by field or attribute name, indicating in which specific field or fields the search term was found. Clicking on an item in the menu will return only those results that match the search term in the specified field. Clicking the
Search icon will return 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.

Go to Advanced Search

Search by Sequences

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.

Read Tutorial

Advanced Search - Sequence Search

Chemical Sketch Tool

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.

Chemical Sketch Tool

Chemical Sketch Documentation

Search by Unreleased & Access New Entries

The PDB archive is updated weekly in two phases

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.

As of Tue May 17 2022 there are 190639 structures.

PDB Data Distributions

The PDB Data Distributions feature on the home page allows you to quickly view the archive in a series of pie charts. Each chart displays a statistical drilldown of the data in the following categories:

  • Scientific Name of Source Organism
  • Taxonomy
  • Experimental Method (Broader Categories)
  • Polymer Entity Type
  • Refinement Resolution (Å)
  • Release Date
  • Enzyme Classification Name
  • Symmetry Type
  • SCOP Classification

In addition, the drilldown data includes links to the Search Results page, where the data can be explored in greater detail.

Search PDB Statistics

The PDB Statistics page lists the current holdings in the PDB and various growth statistics and histograms.

View PDB Statistics Page

Search Ligands

Search ligands bound to macromolecules in the PDB by:

  • SMILES String, InChI
  • Chemical Formula
Ligand Search

Search by Drugs & Drug Targets

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

  • Drug: Atorvastatin (Lipitor)

Go to Advanced Search