Build complex queries with Advanced Search

02/19

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

• 12/31 Happy International Year of Crystallography

• 12/24 Annual Report Published

• 12/17 Paper Published

• 12/10 Quick Tour of Search Results

• 12/03 World AIDS Day Symposium

• 11/26 Browse Membrane Transport Proteins

• 11/19 Help Desk Questions and Answers

• 11/12 Upcoming Meeting: ABRCMS

• 11/05 Comparison Tool for Exploring Sequence and Structure Alignments

• 10/29 Find Structures Using the Protein Symmetry Browser

• 10/22 Fall Newsletter Published

• 10/15 Search by Gene Name

• 10/08 Find Drugs in the PDB

• 10/08 Retirement of SOAP Services

• 10/01 New PDB-101 Animation

• 09/24 wwPDB Public Symposium

• 09/24 Workshop on Theoretical Model Validation and PDBx/mmCIF Data Exchange Format

• 09/24 Beta #11 of the RCSB PDB Mobile Android App is Available

• 09/17 wwPDB Public Symposium

• 09/17 Improved Searching with New Sequence Identity Cutoff

• 09/10 Poster Prize Awarded at ECM

• 09/10 New Website Release

• 09/03 Head Back to School with PDB-101

• 08/27 Map PDB Structures to Full-length Protein Sequences

• 08/20 Join the RCSB PDB Team

• 08/20 Poster Prize Awarded at ISGO

• 08/20 Explore Gallery View of Search Results

• 08/13 Poster Prize Awarded at ACA, ISMB

• 08/13 NOTICE: RCSB PDB Deposition Service Interruption

• 08/06 Ligand Reports

• 07/30 Smart Searching with the Top Bar Suggestion Box

• 07/23 Upcoming Meeting: ICSG2013-SLS

• 07/23 Beta version #4 of RCSB PDB Mobile for Android

• 07/23 Join the RCSB PDB Team

• 07/16 Upcoming Meetings: ACA & ISMB/ECCB

• 07/09 Spring Newsletter Published

• 07/09 Beta version #3 of RCSB PDB Mobile for Android

• 07/02 Build 3D Paper Models at PDB-101

• 06/25 Keep Up-to-Date with the RCSB PDB

• 06/18 Create High Resolution Images

• 06/11 Search the PDB Using Drill-down Pie Charts

• 06/11 New Paper: Trendspotting in the PDB

• 06/04 Map PDB Structures to Full-length Protein Sequences

• 05/28 Browse the Anatomical Therapeutic Chemical Classification System to Find Structures

• 05/21 Web Services for Accessing PDB Data

• 05/14 Personalize the RCSB PDB

• 05/07 New PDB-101 Features

• 04/30 Updated Version of MAXIT Available

• 04/23 Rutgers Day (April 27)

• 04/23 Beta Test RCSB PDB Mobile for Android

• 04/23 DNA Day 2013: April 25

• 04/16 Upcoming Meeting: Experimental Biology and ASBMB

• 04/09 Visit the RCSB PDB at NSTA

• 04/09 Spring Newsletter Published

• 04/02 Search, View Annotations, and Visualize Peptide-like Antibiotic and Inhibitor Molecules

• 03/26 3D Visualization of Protein Symmetry

• 03/19 Distribution of PDB Data by Protein Stoichiometry and Symmetry

• 03/19 Visit the San Diego Festival of Science and Engineering on March 23

• 03/12 Access Drugs and Drug Targets in the PDB

• 03/05 New Website Release

• 02/26 Browse the PDB by GO Terms, EC Number, Source Organism, and More

• 02/19 Build complex queries with Advanced Search

• 02/12 Poster Prize Awarded at AsCA

• 02/05 Author Profiles: Timeline Display of a Researcher's Structures

• 02/05 News Reader Survey

• 01/29 Join the RCSB PDB Team

• 01/29 Visit the Biomolecular Discovery Dome at Biophysical Society

• 01/22 Revision History Widget

• 01/22 Portable Molecules (of the Month)

• 01/15 Quick Tour of Search Results

• 01/08 News Reader Survey

• 01/08 Winter Newsletter Published

• 01/01 Annual Report Published