Browsing School of Medicine & Medical Science by Author "Shields, Denis C."

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Browsing School of Medicine & Medical Science by Author "Shields, Denis C."

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CycloPs : generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids

Duffy, Fergal J. ; Verniere, Mélanie ; Devocelle, Marc ; Bernard, Elise ; Shields, Denis C. ; Chubb, Anthony J. (ACS Publications, 2011-03-24)

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 ...
Prediction of short linear protein binding regions

Mooney, Catherine ; Pollastri, Gianluca ; Shields, Denis C. ; Haslam, Niall J. (Elsevier, 2012-01-06)

Short linear motifs in proteins (typically 3–12 residues in length) play key roles in protein–protein interactions by frequently binding specifically to peptide binding domains within interacting proteins. Their tendency ...
Predictive modelling of angiotensin converting enzyme inhibitory dipeptides

Norris, Roseanne ; Casey, Fergal ; FitzGerald, Richard ; Shields, Denis C. ; Mooney, Catherine (Elsevier, 2012-08-14)

The ability of docking to predict angiotensin converting enzyme (ACE) inhibitory dipeptide sequences was assessed using AutoDock Vina. All potential dipeptides and phospho-dipeptides were docked and scored. Peptide intestinal ...
Profile-based short linear protein motif discovery

Haslam, Niall J. ; Shields, Denis C. (BioMed Central Ltd, 2012-05-18)

Background: Short linear protein motifs are attracting increasing attention as functionally independent sites, typically 3-10 amino acids in length that are enriched in disordered regions of proteins. Multiple methods have ...
Profile-based short linear protein motif discovery.

Haslam, Niall J. ; Shields, Denis C. (BioMed Central, 2012-05-18)

Background Short linear protein motifs are attracting increasing attention as functionally independent sites, typically 3-10 amino acids in length that are enriched in disordered regions of proteins. Multiple methods ...
Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins

Stavropoulos, Ilias ; Khaldi, Nora ; Davey, Norman E. ; O'Brien, Kevin ; Martin, Finian ; Shields, Denis C. (PLOS, 2012-09-04)

Intracellular juxtamembrane regions of transmembrane proteins play pivotal roles in cell signalling, mediated by protein-protein interactions. Disordered protein regions, and short conserved motifs within them, are emerging ...
SLiMSearch 2.0 : biological context for short linear motifs in proteins

Davey, Norman E. ; Haslam, Niall J. ; Shields, Denis C. ; Edwards, Richard J. (Oxford University Press, 2011-05-26)

Short, linear motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch 2.0 (Short, Linear Motif Search) web server allows researchers to identify occurrences of a user-defined SLiM in a proteome, ...
Towards the Improved Discovery and Design of Functional Peptides: Common Features of Diverse Classes Permit Generalized Prediction of Bioactivity

Mooney, Catherine ; Haslam, Niall J. ; Pollastri, Gianluca ; Shields, Denis C. (PLOS, 2012-10)

The conventional wisdom is that certain classes of bioactive peptides have specific structural features that endow their particular functions. Accordingly, predictions of bioactivity have focused on particular subgroups, ...