Improved Ligand Searching

03/09

Searching for ligands using the RCSB PDB's Advanced Search,  Chemical Structure Search, or top-bar pulldown search has been improved.

The "Chemical Name" search from the top-bar pulldown on every page returns matches to names of small molecules in the wwPDB Chemical Component Dictionary and any synonyms.  Searches by Chemical Name or ID will return structures with matching chemical components that are free ligands or are part of a protein or nucleic acid chain.

In the Advanced Search, searches can be specified to look for free and/or polymeric chemical components.  A "sounds like" option searches for misspelled or incomplete chemical component names.  Advanced Searches using SMILES strings use a similarity (instead of dissimilarity) threshold while specifying polymeric type.

The Chemical Structure Search utilizes the latest version of the ChemAxon MarvinSketch applet (5.3.0.1).  Tutorials and screencasts are available to help explore these features.

A detailed description with examples of these new features is available.

For an overview of all recently-added features, see the New Features widget box on the home page or click here.

News Index

• 12/28 Happy Holidays

• 12/21 Deposition Session Restart IDs

• 12/14 Annual Report Published

• 12/07 Poster Prize Awarded at AsCA

• 12/07 Latest Website Release

• 11/30 Learn About Viruses

• 11/30 New and Improved Web Services for Accessing PDB Data

• 11/23 New Ligand Summary Pages

• 11/16 Explore Search Results Using Data Distribution Summaries

• 11/09 Creating Tabular Reports

• 11/02 PDBMobile

• 10/26 Newsletter Published

• 10/19 Binding Affinity Data Integrated with RCSB PDB

• 10/12 Categorized View of Molecule of the Month

• 10/05 Latest Website Release

• 09/28 Poster Prize Awarded at ECM

• 09/28 Analyze small molecule interactions in the PDB with Ligand Explorer

• 09/21 Redesigned BioSync

• 09/14 Exploring Search Results

• 09/07 Tools for Education

• 08/31 Newsletter Published

• 08/24 New Flyers Available

• 08/24 Poster Prize Awarded at ACA

• 08/17 Upcoming Meeting: PDB Symposium at ACS

• 08/10 wwPDB News: Validation Report PDFs

• 08/10 ADIT 2.0 Offers Improved Deposition Process

• 08/03 Poster Prize Awarded at ISMB

• 07/27 Looking at Structures: A Resource for Learning About PDB Data

• 07/27 Paper Published

• 07/20 Upcoming Meeting: ACA

• 07/20 New Release of pdb_extract Available Online and for Download

• 07/13 Get the Latest wwPDB News

• 07/06 Improved Version of ADIT Available

• 07/06 ISMB and 3DSIG Meetings

• 06/29 Version 2 NMR Restraint Files Available from the wwPDB FTP

• 06/29 Use Ligand Expo When Depositing Structures with Ligands

• 06/22 Latest Structures Widget

• 06/15 Papers published

• 06/08 Improved Version of ADIT Available, Transitional Implementation Starts June 14

• 06/08 New Website Features

• 06/01 Create a Collage of Structures

• 05/25 Search the RCSB PDB in Your Web Browser

• 05/18 Turn Your Computer into a PDB Structure Kiosk

• 05/11 New Website Features and Widgets

• 05/04 Version 2 NMR Restraint Files to be Released in the wwPDB FTP on June 30, 2010

• 05/04 wwPDB To Provide Validation Reports as PDFs

• 04/27 Newsletter Published

• 04/20 Screencasts Demonstrate RCSB PDB Features

• 04/20 DNA Day: April 23

• 04/13 Come build virus models at Rutgers Day (April 24)

• 04/13 Exhibiting at Experimental Biology (April 24-28)

• 04/06 Bookmark and Share RCSB PDB Webpages

• 03/30 Advanced Search: Sequence Motif

• 03/23 West Windsor Plainsboro High School North Wins New Jersey Science Olympiad Protein Modeling State Finals

• 03/23 San Diego Science Festival Expo Day: March 27

• 03/16 Exhibiting at NSTA

• 03/09 Improved Ligand Searching

• 03/02 New Website Features

• 02/23 Changes to the wwPDB Policy for Depositing Polypeptide Structures

• 02/23 Online Narrated Tutorial Demonstrates How to Use the RCSB PDB

• 02/16 Exhibition at the Biophysical Society Meeting

• 02/09 Poster Download: How Do Drugs Work?

• 02/02 wwPDB FTP Advisory Notice

• 02/02 Newsletter Published

• 01/26 Comparison Tool for Exploring Sequence and Structure Alignments

• 01/19 NJ Science Olympiad Protein Modeling Results

• 01/12 Time-stamped Copies of PDB Archive Available via FTP

• 01/05 2009 Annual Report Published