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

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

doi:10.1093/nar/gkw366

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

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

Research output: Contribution to journal › Article › peer-review

48 Scopus citations

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.

Original language	English (US)
Pages (from-to)	W522-W528
Number of pages	1
Journal	NUCLEIC ACIDS RESEARCH
Volume	44
Issue number	W1
DOIs	https://doi.org/10.1093/nar/gkw366
State	Published - Apr 30 2016
Externally published	Yes

Bibliographical note

KAUST Repository Item: Exported on 2022-06-01
Acknowledged KAUST grant number(s): KUK-I1-012-43
Acknowledgements: Epigenomics Flagship Project (EPIGEN); KAUST [KUK-I1-012-43]. Funding for open access charge: Epigenomics Flagship Project (EPIGEN).
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

ASJC Scopus subject areas

Genetics

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10.1093/nar/gkw366

Cite this

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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.",

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AU - Lepore, Rosalba

AU - Tramontano, Anna

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

Abstract

Bibliographical note

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