Sequence Alignments in Search Results

10/20

Use the Advanced Search>Sequence option to search protein, DNA, or RNA sequences using mmseqs2 software. A description of this functionality is available.

The search results include a graphic display of sequence alignments. Please adjust the "Display Results as" menu to "Polymer Entities". Zoom using the mouse scroll (wheel) or the mousepad/touchpad to show the amino acid sequence and mismatches.

Zoom using the mouse scroll (wheel) or the mousepad/touchpad to show the amino acid sequence and mismatches. Help documentation is available.

Advanced Search Query Builder can be used combine these Sequence Searches with other types of searches using Boolean operators (AND/OR/NOT):

• Attribute searching: specific fields or full-text search across all fields, such as ID, deposition information, entry features, and experimental information
• Sequence searching: based on a FASTA sequence (with E-value or % Identity cutoffs);
• Sequence Motif searching: find short sequence patterns in PDB structure FASTA sequences using Simple, PROSITE, or RegEx syntax
• Structure Similarity searching: based on an existing Chain or Assembly of a PDB structure
• Chemical Search: find chemical components by Formula or descriptor

New Features Index

• 12/09 Explore Genome-Protein Relationships

• 12/03 Legacy API Shutdown December 9

• 11/23 Explore Improved Carbohydrate Data

• 10/27 Building Advanced Searches

• 10/20 Sequence Alignments in Search Results

• 10/13 Build Customize Tabular Reports of PDB Data

• 10/02 Documentation for New and Improved APIs

• 09/25 Search by Chemical Formula or Descriptor

• 09/22 wwPDB News: Updated Validation Reports for Released PDB Structures

• 09/16 Announcement: Legacy MyPDB Will Be Discontinued October 2020

• 08/25 Explore Sequence-Structure Relationships

• 08/11 Real Time Structural Search of the PDB

• 07/28 wwPDB News: Access Improved Carbohydrate Data at the PDB

• 07/21 Integrating PDB Data with NIH Common Fund Data Resources

• 07/08 Introducing a New Molecular Display

• 06/09 Sequence Motif Searching

• 05/12 Enter the Coronavirus CellPAINT Contest

• 05/07 Announcement: Legacy MyPDB Will Be Discontinued October 2020

• 05/05 Announcement: Legacy RCSB PDB APIs Will Be Discontinued November 2020

• 05/01 June 1: Retirement of Protein Workshop and Ligand Explorer

• 04/15 New APIs Replace REST Services

• 03/25 COVID-19/SARS-CoV-2 Resources

• 02/18 Improve Your Coordinates, Keep Your ID (Phase II)

• 01/14 NMR data distribution in a unified format at the PDB

• 01/08 Time-stamped Copies of PDB and EMDB Archives