Design of protein-protein interaction (PPI) inhibitors is a key challenge in structural bioinformatics and computer-aided drug design. Peptides, which partially mimic the interface area of one of the interacting proteins, are natural candidates to form protein-peptide complexes…
Multi-VORFFIP
Web

Multi-VORFFIP

Predicts protein-protein, protein-peptide, protein-DNA and protein-RNA binding…

Predicts protein-protein, protein-peptide, protein-DNA and protein-RNA binding sites. Multi-VORFFIP utilizes a wide range of structural, evolutionary, experimental and energy-based information that…

PepComposer
Web

PepComposer

A pipeline for the computational design of peptides binding to a given protein…

A pipeline for the computational design of peptides binding to a given protein surface. PepComposer only requires the target protein structure and an approximate definition of the binding site as…

PeptiMap
Web
Desktop

PeptiMap

A protocol for the accurate mapping of peptide binding sites on protein…

A protocol for the accurate mapping of peptide binding sites on protein structures. PeptiMap is based on experimental evidence that peptide-binding sites also bind small organic molecules of various…

GalaxyPepDock
Web

GalaxyPepDock

Performs similarity-based docking by finding templates from the database of…

Performs similarity-based docking by finding templates from the database of experimentally determined structures and building models using energy-based optimization that allows for structural…

CABS-dock
Web

CABS-dock

Given a protein receptor structure and a peptide sequence, CABS-dock performs…

Given a protein receptor structure and a peptide sequence, CABS-dock performs docking search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor…

FlexPepDock
Web

FlexPepDock

A high-resolution peptide docking (refinement) protocol, implemented within the…

A high-resolution peptide docking (refinement) protocol, implemented within the Rosetta framework.

PEP-SiteFinder
Web

PEP-SiteFinder

A service to identify candidate protein-peptide interaction sites.

A service to identify candidate protein-peptide interaction sites.

PepCrawler
Web

PepCrawler

A tool for deriving binding peptides from protein-protein complexes and…

A tool for deriving binding peptides from protein-protein complexes and prediction of peptide-protein complexes, by performing high-resolution docking refinement and estimation of binding affinity.

PepSite
Web

PepSite

It can be used to predict peptide-binding spots from protein surfaces alone.

It can be used to predict peptide-binding spots from protein surfaces alone.

pepATTRACT
Desktop
Web

pepATTRACT

Generates a fully blind peptide-protein docking protocol for usage with the…

Generates a fully blind peptide-protein docking protocol for usage with the ATTRACT program. The ATTRACT Easy web interface provides a convenient way to set up an ab-initio two-body protein-protein…

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