Protein-peptide docking software tools | Interaction data analysis
Protein–peptide interactions are involved in a wide range of biological processes and are attractive targets for therapeutic purposes because of their small interfaces. Therefore, effective protein–peptide docking techniques can provide the basis for potential therapeutic applications by enabling an atomic-level understanding of protein interactions. With the increasing number of protein–peptide structures deposited in the protein data bank, the prediction accuracy of protein-peptide docking can be enhanced by utilizing the information provided by the database.
Performs docking search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. CABS-dock employs an efficient peptide docking scheme. It permits initial-stage prediction of the (CABS-dock peptide) SLiM binding mode and identification of protein-protein interaction (PPI) interface localization. This tool can be modified or combined with more sophisticated procedures for computation modeling of protein interactions.
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 flexibility. GalaxyPepDock can therefore effectively model the structural differences between the template and target protein–peptide complexes. The performance of GalaxyPepDock is superior to those of the other currently available web servers when tested on the PeptiDB set and on recently released complex structures. When tested on the CAPRI target 67, GalaxyPepDock generates models that are more accurate than the best server models submitted during the CAPRI blind prediction experiment.
Models peptide conformations and sequent global sampling of binding orientations for blind and flexible peptide docking. HPEPDOCK can serve for local peptide docking if information about the binding site is available. It can integrate the available peptide binding information from the Protein Data Bank (PDB). This tool is based on a hierarchical flexible-peptide docking protocol that includes different functions to work.
Gives a heuristic solution to a computationally hard problem (NPC). CombDock is an algorithm for the automated assembly of protein substructures. This application is able to predict near-native assemblies for various examples of both domains and to build blocks with different levels of distortion. It can also be used in protein structure prediction if the local structural units are given and assist in obtaining a structural model.
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