Tour of Ligand Deposition

12/08

wwPDB launched the Deposition Tool for structures determined using X-ray crystallography on January 27, 2014 as part of a new Deposition and Annotation System. Since then, more than 10,200 structures have been deposited and annotated, and more than 5,600 structures released in the archive using this system.

Videos demonstrate how to review and submit ligands with the wwPDB Deposition Tool.

For all ligands present in the uploaded coordinate file, the deposition system will search for graphical matches against all released ligands in the PDB. Close (but not exact) matches will require depositor attention as demonstrated here:

When the system cannot find a match for a ligand, depositors will be required to provide a SMILES or InChI string or a 2D chemical drawing, as shown in this video:

The wwPDB Deposition Tool is used for X-ray crystallographic data; similar tools for NMR and 3DEM will be available in 2016.  Up-to-date information about the Deposition Tool, tutorials for getting started, and an FAQ are available from the wwPDB website.

News Index

• 12/29 Happy Holidays

• 12/22 Poster Prize Awarded at AsCA

• 12/15 Smart Searching

• 12/08 Tour of Ligand Deposition

• 12/01 Validate Before Depositing to Save Time

• 11/24 Advanced Search: Multiple ID Search

• 11/17 Comparison Tool for Exploring Sequence and Structure Alignments

• 11/10 Visualize Structure Quality and Mutations with Protein Feature View

• 11/03 Structure Summary Pages Redesigned

• 10/27 Upcoming Meeting: SACNAS

• 10/20 Molecular Origami: Insulin

• 10/13 Fall Newsletter Published

• 10/06 Access New Website Features

• 09/29 Poster Prize Awarded at ISMB/ECCB

• 09/22 Poster Prize Awarded at ECM29

• 09/15 RCSB PDB Software Shared on GitHub

• 09/08 Head Back to School with PDB-101

• 09/01 Poster Prize Awarded at ACA

• 08/25 Annual Report Published

• 08/18 Take an Interactive Tour of the Protein Data Bank

• 08/11 Save References to Mendeley and Endnote

• 08/04 Explore PDB Structures by Browsing Annotations

• 07/28 Web Services for Accessing PDB Data

• 07/21 Summer Newsletter Published

• 07/14 Membrane Query and Annotation

• 07/07 Poster Prize Awarded at ICSG

• 07/07 wwPDB Deposition Tool Replaces ADIT for Crystal Structures

• 06/30 Contact Customer Services with Questions and Feedback

• 06/23 Map Genomic Position to Protein Sequence and Structure

• 06/16 HIV Video Challenge Awards

• 06/09 Science Olympiad National Protein Modeling Results

• 06/02 Vote Now!

• 05/26 Visualize in 3D with PV

• 05/19 Download Batches of Data

• 05/12 Molecule of the Month Paper Published

• 05/05 HS Video Challenge Deadline: May 31

• 05/05 Experience the Art of Science

• 04/28 Join our Development Team in San Diego

• 04/28 Access New Website Features

• 04/21 Rutgers Day (April 27)

• 04/21 DNA Day 2015: April 25

• 04/14 Education Corner: The Science of HIV

• 04/07 Spring Newsletter Published

• 03/31 Take an Interactive Tour of the Protein Data Bank

• 03/24 Build 3D Paper Models of Biomolecules

• 03/24 Join the RCSB PDB Team

• 03/17 Visit the San Diego Festival of Science and Engineering on March 22

• 03/10 2015 High School Video Challenge

• 03/03 San Diego Science Olympiad Protein Modeling Results

• 03/03 New Publications

• 02/24 Exploring Structure Quality

• 02/17 2015 High School Video Challenge Materials

• 02/10 BioJava 4.0.0 Released

• 02/03 NJ Science Olympiad Protein Modeling Results

• 01/27 wwPDB Deposition Tool Replaces ADIT for Crystal Structures

• 01/20 RCSB PDB Mobile for iOS and Android Update

• 01/13 Winter Newsletter Published

• 01/06 New Calendar Celebrates 15th Anniversary of Molecule of the Month

• 01/06 Video Challenge for High School Students