Binding Site Visualization

01/28

Options for visualizing binding sites have been added to the Jmol options available at rcsb.org.

From a Structure Summary page (example: 1stp), select the option for "3D View" listed under the entry's image (or from the 3D View tab).

Options for viewing domains and ligands are at the bottom of the page.

Select the Ligand tab and then the link to "View Pocket in Jmol" to access this new feature.  Residues are displayed in contact with the selected ligand. A cropped ligand van der Waals surface will appear that is color coded by the proximity to the van der Waals surface of the binding site (red: close contact, blue: far contact).

Thanks to Robert Hanson (St. Olaf College), the current principal Jmol developer, for implementing this feature during his visit to the RCSB PDB.

The biotin binding site in PDB entry 1stp. To access this view, select the 'Ligands' tab and click on 'View Pocket in Jmol'.

News Index

• 12/30 Happy Holidays

• 12/23 Congratulations to 2014 Poster Prize Winners

• 12/23 ADIT To Be Retired for Depositions from X-ray Crystallography

• 12/16 Contact Customer Services with Questions and Feedback

• 12/09 Save References to Mendeley and Endnote

• 12/09 Inclusion of Large Structures in the PDB Archive

• 12/02 Join the RCSB PDB Team

• 12/02 Art of Science on Display

• 12/02 World AIDS Day Symposium

• 11/25 Dr Frank Allen 1944-2014

• 11/25 ADIT To Be Retired for Depositions from X-ray Crystallography

• 11/18 RCSB PDB Software Shared on GitHub

• 11/11 RCSB PDB Reference in the Top 100

• 11/11 New Website Release

• 11/04 Join the Conversation

• 10/28 Membrane Query and Annotation

• 10/28 Web Services for Accessing PDB Data

• 10/21 Comparison Tool for Exploring Sequence and Structure Alignments

• 10/14 Upcoming Meeting: SACNAS

• 10/07 Fall Newsletter Published

• 09/30 Map Structures to Sequences with Protein Feature View

• 09/23 Paper Published: RCSB PDB Mobile

• 09/16 Exploring Structure Quality

• 09/09 Head Back to School with PDB-101

• 09/02 Take the PDB-101 Survey

• 09/02 Join the RCSB PDB Team

• 08/26 Announcement: Meeting on Hybrid Methods

• 08/26 Poster Prize Awarded at ISMB

• 08/19 Poster Prize Awarded at IUCr

• 08/12 New Website Release

• 08/05 wwPDB Events at IUCr (August 5-12)

• 07/29 Personalize the RCSB PDB

• 07/22 Explore PDB Structures by Browsing Annotations

• 07/15 RCSB PDB Leadership Transition

• 07/08 Summer Newsletter Published

• 07/01 Quick Tour of Search Results

• 06/24 Depositing Data? Use the wwPDB Deposition & Annotation System

• 06/17 HIV Video Challenge Awards

• 06/10 Papers Published

• 06/10 Poster Prize Awarded at ACA

• 06/03 Vote Now!

• 05/27 RCSB PDB Mobile for iOS and Android

• 05/20 Art of Science Travels to Paris, France

• 05/20 Special Events in Albuquerque at ACA 2014

• 05/13 Molecular Machinery Update

• 05/13 PDB Reaches 100,000

• 05/06 Video Challenge for High School Students

• 04/29 New Website Release

• 04/22 DNA Day 2014: April 25

• 04/22 Visit the USA Science and Engineering Festival Expo on April 26 & 27

• 04/15 Resources for High School Video Challenge

• 04/08 Spring Newsletter Published

• 04/01 Our Best Wishes to Phil

• 04/01 Build a Model of GFP

• 03/25 The Art of Systems Biology and Nanoscience

• 03/25 Learn How to Create Molecular Animations

• 03/18 Visit the San Diego Festival of Science and Engineering on March 22

• 03/11 Meet the RCSB PDB Team

• 03/11 Author Profiles: Timeline Display of a Researcher's Structures

• 03/04 Membrane Query and Annotation

• 02/25 Video Challenge for High School Students

• 02/18 Releasing Structures on Hold for Publication

• 02/11 Find PDB Structures with Protein Purification Tags

• 02/04 Tour of Ligand Deposition

• 01/28 Binding Site Visualization

• 01/21 Big Picture on Proteins

• 01/14 RapiData 2014

• 01/14 Teacher Workshop in Boulder, Colorado

• 01/07 Winter Newsletter Published