Ligand Searching

11/13

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Learn more about the the active form of vitamin D found in the body (ID: VDX) in November's Molecule of the Month feature.

Quickly find small molecule components found in PDB entries using any of these tools:

• Simple top bar searching (with autocomplete suggestions)

Click on the Ligand icon to limit your search. Enter a ligand name or the 3-character chemical component ID.

• Chemical Component Search

This powerful form can be accessed by selecting the top bar ligand icon and then [ additional ligand options ]. Launch the chemical structure editor to draw a structure, or paste in a SMILES or SMARTS string, and then perform a substructure, exact, similarity, or superstructure search. In addition, ligands can be searched by name, identifier, formula, and molecular weight.  A tutorial demonstrating this search is available.

• Advanced Search

Supports the searches mentioned above, as well as queries by chemical component type, binding affinity, sub-component, and more. These types of searches can be combined and even amended with searches for the associated structures. Learn more about Advanced Search with this tutorial and list of available queries.

Ligand searches return the corresponding Ligand Summary page that contains an overview of the chemical component, 2D and 3D images, links to other resources, and links to related ligands and PDB entries.

All residues and small molecule components found in PDB entries, including standard and modified amino acids/nucleotides, small molecule ligands, ions, and solvent molecules, are described in the wwPDB's Chemical Component Dictionary.

News Index

• 12/25 Happy Holidays

• 12/18 Join the RCSB PDB Team

• 12/18 Papers Published

• 12/11 Announcement: Meeting on Hybrid Methods

• 12/11 Map PDB Structures to Full-length Protein Sequences

• 12/04 Advanced Search: Multiple ID Search

• 11/27 World AIDS Day: December 1

• 11/27 MyPDB: Keep up-to-date with new structures... automatically!

• 11/20 Educational Activities and Lessons

• 11/20 Take our quick survey

• 11/13 Take our quick survey

• 11/13 Ligand Searching

• 11/06 Explore Gallery View of Search Results

• 10/30 Improved Drug Searches and Annotations

• 10/23 New Website Release

• 10/16 Nobel Prize Awarded for studies of G-protein-coupled receptors

• 10/16 Explore the Structural Biology of HIV

• 10/09 Fall Newsletter Published

• 10/02 Advanced Search: Sequence Motif

• 10/02 Turn Your Computer into a PDB Structure Kiosk

• 09/25 Explore PDB Data Overviews

• 09/18 High Resolution Images at the RCSB PDB

• 09/11 Poster Prize Awarded at ECM

• 09/11 Customized Home Page: Structure Comparison Tool

• 09/04 Head Back to School with PDB-101

• 08/28 Smart Searching with the Top Bar Suggestion Box

• 08/21 Download RCSB PDB Mobile for the iPhone/iPad

• 08/21 Poster Prize Awarded at ACA

• 08/14 Poster Prize Awarded at ISMB

• 08/14 Improved Ligand Reports

• 08/07 Build complex queries with Advanced Search

• 07/31 Prepare data for deposition with pdb_extract and SF-Tool

• 07/31 Protein Society Annual Symposium

• 07/24 Upcoming Meeting: ACA

• 07/17 Different Ways To Explore New Entries

• 07/10 ISMB and 3DSIG Meetings

• 07/10 Summer Newsletter Published

• 07/03 Author Profiles: Timeline Display of a Researcher's Structures

• 06/26 Latest Website Release

• 06/19 Personalize the RCSB PDB with MyPDB

• 06/19 National Protein Modeling Champions

• 06/12 Top Bar SMILES String Searching

• 06/05 Molecule of the Month reaches 150

• 05/29 Tour the PDB with Drill-down Pie Charts

• 05/22 Domain-based Structural Alignments

• 05/15 New Poster: Virus Structures

• 05/08 Bookmark and Post Webpages

• 05/08 Customized Home Page: Sequence Search

• 05/01 Latest Website Release

• 04/24 Rutgers Day (April 28)

• 04/24 Create a Collage of Structures

• 04/17 DNA Day 2012: April 20

• 04/17 Exhibiting at Experimental Biology

• 04/10 Spring Newsletter Published

• 04/03 Depositing Structures with Ligands

• 03/27 Browse the PDB by GO Terms, EC Number, Source Organism, and More

• 03/20 Visit the San Diego Festival of Science and Engineering on March 24

• 03/20 J.P. Stevens HS Wins NJ Protein Modeling Event

• 03/13 Sound Science

• 03/13 PDBMobile and iOS 5.1

• 03/13 Preview New 3D Similarity Tab

• 03/06 Explore a Structural View of Biology at PDB-101

• 02/28 Visualize Molecular Surfaces with Protein Workshop

• 02/21 New Structures Widget

• 02/21 Visit the Biomolecular Discovery Dome at Biophysical Society

• 02/14 Ligand Summary Pages

• 02/07 Free Webinar and Updated Tutorial

• 02/07 Volunteer Structures For Foldit

• 01/31 Announcement: Meeting on Hybrid Methods

• 01/31 Free Webinar on How to use the RCSB PDB

• 01/24 Newsletter Published

• 01/17 NJ Science Olympiad Protein Modeling Results

• 01/10 Web Services for Accessing PDB Data

• 01/03 Annual Report Published