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.

PepComposer: computational design of peptides binding to a given protein surface / Obarska-Kosinska, Agnieszka; Iacoangeli, Alfredo; Lepore, Rosalba; Tramontano, Anna. - In: NUCLEIC ACIDS RESEARCH. - ISSN 0305-1048. - 44:W1(2016), pp. 522-528. [10.1093/nar/gkw366]

PepComposer: computational design of peptides binding to a given protein surface

Obarska-Kosinska, Agnieszka;Iacoangeli, Alfredo;Lepore, Rosalba
;
Tramontano, Anna
2016

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.
2016
Protein design; molecular interactions; monte carlo simulation; computer-aided design; computational modelling
01 Pubblicazione su rivista::01a Articolo in rivista
PepComposer: computational design of peptides binding to a given protein surface / Obarska-Kosinska, Agnieszka; Iacoangeli, Alfredo; Lepore, Rosalba; Tramontano, Anna. - In: NUCLEIC ACIDS RESEARCH. - ISSN 0305-1048. - 44:W1(2016), pp. 522-528. [10.1093/nar/gkw366]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/1680142
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