Find Similar Proteins

Find proteins with similar sequences using the RCSB PDB sequence search.

Menu: Proteins → Search → Find Similar Proteins

This tool also uses US-align to perform structural alignment. Aligned structures will be added to the project.

Where to find it

Parameter	Default	Description
Query source	`project`	Choose whether to use proteins from the project or to provide FASTA text.
Proteins to use as queries	—	—
FASTA sequence(s) to use as queries	—	Paste one or more protein sequences in FASTA format. Each sequence should start with a '>' header line.
E-value cutoff	`0.1`	Maximum E-value for a match to be considered significant.
Sequence identity cutoff (%)	`UserArgType.Text`	Minimum sequence identity required for a match.
Maximum results per query	`UserArgType.Alert`	The maximum number of similar proteins to retrieve for each query protein.
Has Ligand(s)	No	Only return proteins that contain non-polymer ligands (molecular weight ≥ 150 Da).
Download structures	Yes	Download all protein structures into the project.
Align structures	Yes	Align structures to their respective query proteins. For FASTA queries, aligns to the top search result.