title: PepComposer: computational design of peptides binding to a given protein surface.
abstract: There is a wide interest in designing peptides able to bind to a specific region of a protein with the aim of interfering with a known interaction or as starting point for the design of inhibitors. Here we describe PepComposer, a new 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 input. We first retrieve a set of peptide backbone scaffolds from monomeric proteins that harbor the same backbone arrangement as the binding site of the protein of interest. Next, we design optimal sequences for the identified peptide scaffolds. The method is fully automatic and available as a web server at http://biocomputing.it/pepcomposer/webserver.
authors.affiliation: Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Obarska-Kosinska
authors.affiliation: Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Iacoangeli
authors.affiliation: Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy alba.lepore@uniroma1.it.
authors.forename: Rosalba
authors.initials: R
authors.lastname: Lepore
authors.affiliation: Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy Istituto Pasteur-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Tramontano
mesh_terms: D001331:Automation; D001665:Binding Sites; D017076:Computer-Aided Design; D029968:Escherichia coli Proteins / Q000737:chemistry; D036781:Fimbriae Proteins / Q000737:chemistry; D020407:Internet; D008958:Models, Molecular; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software; D013816:Thermodynamics; D017361:Viral Nonstructural Proteins / Q000737:chemistry; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D029968:Escherichia coli Proteins; D036781:Fimbriae Proteins; D010455:Peptides; D011506:Proteins; D017361:Viral Nonstructural Proteins; C529458:FimG protein, E coli; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases