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FoldSeek

Some types of search, such as by sequence or structure similarity, require specialized tools. Foldseek is a fast and reliable protein structure similarity lookup algorithm.

How to Use FoldSeek

Find others like 3kwd

3kwd

FoldSeek runtimes scales with the size of the database used. Typically 0.5 to 1.0 min on the PDB.

Inputs

PDB File
Protein structure file.
Database

A specific database to search against. Copilot currently uses PDB as the default.

Outputs

List of Hits
A list of database hits, structurally aligned to the input.
TM-Score

Score of structural identity between two proteins. Ranges from 0.0 to 1.0, with 0.0 being no match, 1.0 being exact match, and 0.5 being same fold/family.

Fident

Percentage sequence identity between the database hit and input after structural alignment. 100 means identical sequence match.

Examples

Find similar proteins to MA998

MA998

Lookup structures like P42212

GFP