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PROPEDIA is a database of protein-peptide interactions. PROPEDIA main goal is to give new insights into peptide design of biotechnological interests.

©2026 Propedia v3.26.825 | Laboratory of Bioinformatics and Systems, UFMG (Brazil)
License | GitHub | Propedia v1 | Propedia v2

PROPEDIA is a database of peptide-protein complexes clusterized in three methodologies: based on peptide sequences; based on structure interface; and based on binding sites. PROPEDIA main goal is to give new insights into peptide design of biotechnological interests.

# Created by:
Pedro Martins / Diego Mariano / Raquel C. de Melo-Minardi

# Backend/frontend:
Diego Mariano

Cite:
Martins, P.M., Santos, L.H., Mariano, D. et al. Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm. BMC Bioinformatics 22, 1 (2021). https://doi.org/10.1186/s12859-020-03881-z

Search for similar protein or peptide sequences using BLAST

BLAST algorithm searches for similar protein or peptide sequences by identifying short local matches (words) between the query and database sequences ?.

Input sequence

Search for:
Peptides Proteins

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Search for similar binding sites

The search for similar binding sites in Propedia employs the ProBiS algorithm, which detects local structural similarities by comparing the 3D surface of the queried protein binding site with those of proteins stored in the database.

Enter the PDB code, target protein chain, and binding site residue numbers separated by commas (use hyphens to indicate ranges) ?.

PDB ID

or

Your structure

Use one or the other: a PDB code, which Propedia downloads from the RCSB PDB, or your own structure in PDB format (up to 20 MB), used only for this search and not added to the database.

Chain Only the selected chain is displayed in the viewer.

Use a reference chain to define the binding site ?

Binding site residues

Please, cite Propedia in your publication

We kindly ask that you cite both the original article and the most recent published article from the database. You can cite the other articles if you use data and functionalities from specific versions.
Original paper (2021)
Martins, P.M., Santos, L.H., Mariano, D. et al. Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm. BMC Bioinformatics 22, 1 (2021). doi: 10.1186/s12859-020-03881-z
Propedia v2.3 (2023)
Martins P, Mariano D, Carvalho FC, Bastos LL, Moraes L, Paixão V and Cardoso de Melo-Minardi R (2023). Propedia v2.3: A novel representation approach for the peptide-protein interaction database using graph-based structural signatures. Front. Bioinform. 3:1103103. doi: 10.3389/fbinf.2023.1103103
Propedia 26 (2026)
In development.