Duffy, Fergal J.

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Duffy, Fergal J.
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Duffy, Fergal J.

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  • Publication
    CycloPs : generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids
    (ACS Publications, 2011-03-24)
    Duffy, Fergal J. 
    ;
    Verniere, Mélanie 
    ;
    Devocelle, Marc 
    ;
    Bernard, Elise 
    ;
    Shields, Denis C. 
    ;
    Chubb, Anthony J. 
    We introduce CycloPs, software for the generation of virtual libraries of constrained peptides including natural and nonnatural commercially available amino acids. The software is written in the cross-platform Python programming language, and features include generating virtual libraries in one-dimensional SMILES and three-dimensional SDF formats, suitable for virtual screening. The stand-alone software is capable of filtering the virtual libraries using empirical measurements, including peptide synthesizability by standard peptide synthesis techniques, stability, and the druglike properties of the peptide. The software and accompanying Web interface is designed to enable the rapid generation of large, structurally diverse, synthesizable virtual libraries of constrained peptides quickly and conveniently, for use in virtual screening experiments. The stand-alone software, and the Web interface for evaluating these empirical properties of a single peptide, are available at http://bioware.ucd.ie.
      2623Scopus© Citations 36
  • Publication
    Computational Approaches to Developing Short Cyclic Peptide Modulators of Protein-Protein Interactions
    (Humana Press, 2014)
    Duffy, Fergal J. 
    ;
    Devocelle, Marc 
    ;
    Shields, Denis C. 
    Cyclic peptides are a promising class of bioactive molecules potentially capable of modulating 'difficult' targets, such as protein–protein interactions. Cyclic peptides have long been used as therapeutics derived from natural product derivatives, but remain an underexplored class of compounds from the perspective of rational drug design, possibly due to the known weaknesses of peptide drugs in general. While cyclic peptides are non 'druglike' by the accepted empirical rules, their unique structure may lend itself to both membrane permeability and proteolytic resistance—the main barriers to oral delivery. The constrained shape of cyclic peptides also lends itself better to virtual screening approaches, and new tools and successes in this area have been recently noted. An increasing number of strategies are available, both to generate and screen cyclic peptide libraries, and best practises and current successes are described within. This chapter will describe various computational strategies for virtual screening cyclic peptides, along with known implementations and applications. We will explore the generation and screening of diverse combinatorial virtual libraries, incorporating a range of cyclization strategies and structural modifications. More advanced approaches covered include evolutionary algorithms designed to aid in screening large structural libraries, machine learning approaches, and harnessing bioinformatics resources to bias cyclic peptide virtual libraries towards known bioactive structures.
    Scopus© Citations 13  1342