Build complex queries with Advanced Search

08/07

Click on the magnifying glass icon from the top menu bar to access Advanced Search.

Advanced Search provides the capability of combining multiple searches of specific types of data in a logical AND or OR. The result is a list of structures that comply with ALL or ANY of the search criteria, respectively.

Individual data items are organized by category; contextual help and examples are available by selecting  . New options include quick searches by experimental and/or molecule type, searches based on structure determination method, and the ability to find structures containing interresidue connectivity (LINK records) that cannot be inferred from the primary structure.

Currently, users can build searches based on:

• Quick Search: retrieve all PDB entries or a subset based on experimental method or molecule type
• ID(s) and Keywords: PDB, PubMed, UniProtKB, Pfam IDs; text and keyword searching
• Structure Annotation: structure title, description; and macromolecule name
• Deposition: author name; deposit, release, and revision date; latest released and modified structures; Structural Genomics Project
• Structure Features: macromolecule type; number of chains (asymmetric unit or biological assembly), entities, models, and disulfide bonds; interresidue connectivity (LINK records); molecular weight; secondary structure content; secondary structure length; SCOP, CATH, taxonomy
• Sequence Features: sequence; translated nucleotide sequence; sequence motif; chain length; genome location
• Chemical Components: name; ID; InChi descriptor; SMILES/SMARTS; molecular weight; chemical formula; chemical component type; binding affinity; has ligands; has modified residues; sub-components
• Biology: Source; expression organism; Enzyme Classification; biological process; cell component; molecular function; Transporter Classification
• Methods: experimental method; X-ray resolution, R factor, diffraction source, structure determination method, reflections, cell dimensions, software, space group, crystal properties, detector; EM assembly
• Publication: citation; MeSH terms; PubMed abstract
• Misc: Has external links

The number of entries matching each individual query can be shown before running the full Advanced Search.  Searches can also be filtered by removing sequence similarity.

Advanced Searches can be stored in MyPDB to be run or modified at any time.

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 Take our quick survey

• 11/20 Educational Activities and Lessons

• 11/13 Ligand Searching

• 11/13 Take our quick survey

• 11/06 Explore Gallery View of Search Results

• 10/30 Improved Drug Searches and Annotations

• 10/23 New Website Release

• 10/16 Explore the Structural Biology of HIV

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

• 10/09 Fall Newsletter Published

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

• 10/02 Advanced Search: Sequence Motif

• 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 Poster Prize Awarded at ACA

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

• 08/14 Poster Prize Awarded at ISMB

• 08/14 Improved Ligand Reports

• 08/07 Build complex queries with Advanced Search

• 07/31 Protein Society Annual Symposium

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

• 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 National Protein Modeling Champions

• 06/19 Personalize the RCSB PDB with MyPDB

• 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 Customized Home Page: Sequence Search

• 05/08 Bookmark and Post Webpages

• 05/01 Latest Website Release

• 04/24 Create a Collage of Structures

• 04/24 Rutgers Day (April 28)

• 04/17 Exhibiting at Experimental Biology

• 04/17 DNA Day 2012: April 20

• 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 J.P. Stevens HS Wins NJ Protein Modeling Event

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

• 03/13 PDBMobile and iOS 5.1

• 03/13 Preview New 3D Similarity Tab

• 03/13 Sound Science

• 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 Free Webinar on How to use the RCSB PDB

• 01/31 Announcement: Meeting on Hybrid Methods

• 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