In this chapter, we describe ClusPro, a web server for protein–protein and protein–peptide docking. As an input, the server requires two Protein Data Bank (PDB) files (protein–protein mode) or a PDB file for the protein and a sequence for the ligand (protein–peptide mode). Its ...
molecular dockingmolecular modelingweb serverProtein-peptide interactions play a crucial role in a variety of cellular processes. The protein-peptide complex structure is a key to understand the mechanisms underlying protein-peptide interactions and is critical for peptide therapeutic development. We present...
LEADS-PEP: a benchmark data set for assessment of peptide docking performance J. Chem. Inf. Model., 56 (2016), pp. 188-200 CrossrefView in ScopusGoogle Scholar 37 D.A. Antunes, et al. DINC 2.0: a new protein-peptide docking webserver using an incremental approach Cancer Res. (2017)...
Here we describe an integrated approach called "PeptideMine" for the identification of peptides based on specific functional patterns present in the sequence of an interacting protein. This approach based on sequence searches in the interacting sequence space has been developed into a webserver, which...
The HDOCK server ( http://hdock.phys.hust.edu.cn/ ) is a highly integrated suite of homology search, template-based modeling, structure prediction, macromolecular docking, biological information incorporation and job management for robust and fast protei
compared to 21.1% for pepATTRACT server. HPEPDOCK also performed well in docking against homology models and obtained a success rate of 29.8% within top 10 predictions. For local peptide docking, HPEPDOCK achieved a high success rate of 72.6% on a benchmark of 62 unbound cases within top ...
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-...
Impact of sodium alginate hydrogel containing bacteriophage peptides that specifically bind to the EtCab protein on the inhibition of Eimeria tenella infection Hang Chen Wenjing Zhi Dexing Ma Veterinary Research(2025) A comprehensive survey of scoring functions for protein docking models ...
There are various docking methods to study peptide–protein complexes. Majorly, these methods can be divided into three groups: peptide–protein docking, protein–protein docking, and protein–ligand docking. Among them, peptide–protein docking has specifically been developed to dock peptides on then...
Protein-peptide interactions play an important role in major cellular processes, and are associated with several human diseases. To understand and potentially regulate these cellular function and diseases it is important to know the molecular details of the interactions. However, because of peptide flexi...