What's New

The November 11, 2014 release offers the following new features:


New Redesign Website

Redesigned Home Page

Simple. Clean. Usable. Features and Tools More Visible.


A year ago, as the team discussed RCSB's mission statement of being a premiere scientific site focused on usability and being cutting edge in delivering quality data and advanced tools, we came to a consensus that the site needed to be redesigned. Not just to keep up with current design trends, but to do the following:

  • Reduce information overload and redundancy
  • Organize and group related content
  • Catch all different user groups from high school students to scientists
  • Think through user flow and goals, making it easier to accomplish tasks
  • Addressing user needs: make core features and tool more visible
  • Usher in new yet proven web technology to handle expanding scientific content

After much discussions, team meetings, whiteboard scribbles, prototyping, and hundred of hours of code development and testing, we hope the redesign of our homepage will lead in that direction of being easier to use and more intuitive.

We welcome your feedback. Please leave your feedback and comments on the new site design and layout.


The new home page provides access to all tools and resources in different sections of the home page. All information about specific topics such as Deposit or Search can be browsed or accessed from a single panel.

Menu Bar

RCSB PDB Top Bar Navigation

The menu bar offers quick access to various categories of tools, information, and the MyPDB login. The menu appears across the website to provide constant access to the resources highlighted in the panels section below.



Resources

The current number of PDB entries is displayed to the right of the RCSB PDB logo. Clicking on this link retrieves all structures in the PDB along with a breakdown of the archive by categories (Experimental method, EC classification, etc.).

The small logos link to the corresponding resources: PDB-101 is the educational section of the RCSB PDB, which includes related resources, posters, and the Molecule of the Month series. wwPDB is the international collaboration that manages the PDB archive. EMDataBank is the unified data resource for 3DEM.

RCSB PDB Resources

Search Box Area

Text Search Box

This simple search option queries the archive by

  • Identifiers: PDB ID, PDB Chemical Component ID, UniProt ID, gene ID
  • Names: author, macromolecule, ligand, gene, domain
  • Sequences: protein and nucleotide sequences
  • Linear notations: SMILES strings and molecular formulas (e.g., C6H12O6)

Other Search Options

  • Advanced Search provides more specific and expanded search criteria. Several search criteria can be combined to create complex queries.
  • Browse by Annotations can be used to navigate hierarchical annotations such as Gene Ontologies, Membrane Protein, Transporter Classification, and Enzyme Classification.

Social Media, RCSB PDB Mobile, and GitHub

These icons link to our Facebook, Twitter, and YouTube pages; RCSB PDB Mobile downloads for Apple and Android; and the last icon links to our open source projects in GitHub.

RCSB PDB Search Bar & Social Media


Topic Panels

Topic Panels provide access to RCSB PDB resources to deposit, search, visualize, analyze, download, or learn about macromolecules.

Welcome Panel

By default, the Welcome panel is displayed and with the current Molecule of the Month article.


Other topic panels are briefly described below:

Deposit: The middle column presents different options for data preparation, validation, and deposition, along with related documentation.


Search: The middle column shows RCSB PDB search options (by category, Advanced, sequence, ligand), searchable tables of drugs and drug targets, access to unreleased and new entries, annotation browsers, and PDB statistics.


Visualize: The middle column displays visualization options offered by the RCSB PDB, including 3D viewers and tools for viewing sequence-structure correspondences, and related documentation.


Analyze: The middle column offers tools to analyze sequence and structure alignments, protein symmetry and other featured tools.


Download: The middle column offers tools that perform batch download of structure, sequence, and ligand data, and description of RESTful Web Services.


Learn: The middle column presents the collection of educational materials available from PDB-101, including Molecule of the Month articles and the Structural View of Biology Browser.



What's New Section

This section highlights new entries, new website features, news, newsletters, and other publications by the RCSB PDB and wwPDB.

New Structures

Latest Entries: This widget loops through a random selection of PDB entries from the most recent weekly update. The link: "As of Tuesday..." corresponds to the structures in that update.

New Features

New Features: Links to descriptions of the latest features added to the website.

New Articles

News and Publications: Access to the latest news from the RCSB PDB and the wwPDB. The publications menu offers access to related RCSB PDB publications.



PDB at a Glance

The key statistics shown for the PDB archive link to the corresponding data. A complete list of statistics compiled by the RCSB PDB is available from the "More Statistics" button.

RCSB PDB Statistics


Footer

RCSB PDB Footer

The footer provides quick access to information pages. The "Feedback" button on the bottom right is available from all recently redesigned pages. Use this button to submit feedback or any comments to the RCSB PDB team.



Citation

Reference Management

Quickly save references to Mendeley & EndNote

Download Primary PDB Citations to Mendeley and EndNote

Download Primary PDB Citations to Mendeley and Endnote

Most PDB entries are associated with a primary reference. An option to download citation information (obtained from PubMed, if available) to Mendeley and EndNote reference management programs has been added to Structure Summary pages.

Example of Mendeley import for PDB ID 3J2U.

Example of Mendeley import


RCSB PDB Citation Page

Journal articles and book chapters authored by RCSB PDB members are listed on the Publications page (accessible from the More menu at the top of the page and from the footer).

The readability of the Publication page has been improved.