Denis C. Shields

Publication Activity (10 Years)

Years Active: 1992-2021
Publications (10 Years): 2

Top Topics

Physicochemical Properties

Protein Sequences

Top Venues

J. Chem. Inf. Model.

Nucleic Acids Res.

Publications

Chiara E. Cotroneo, Isobel Claire Gormley, Denis C. Shields, Michael Salter-Townshend
Computational modelling of chromosomally clustering protein domains in bacteria. BMC Bioinform. 22 (1) (2021)
Peter Jehl, Jean Manguy, Denis C. Shields, Desmond G. Higgins, Norman E. Davey
ProViz - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Fergal J. Duffy, Darragh O'Donovan, Marc Devocelle, Niamh Moran, David J. O'Connell, Denis C. Shields
Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals Protein Interfaces Readily Targetable by Cyclic Peptides. J. Chem. Inf. Model. 55 (3) (2015)
Federica Lombardi, Kalyan Golla, Darren J. Fitzpatrick, Fergal P. Casey, Niamh Moran, Denis C. Shields
Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies. PLoS Comput. Biol. 11 (4) (2015)
Emily Olorin, Kevin T. O'Brien, Nicolas Palopoli, Åsa Pérez-Bercoff, Denis C. Shields, Richard J. Edwards
SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks. F1000Research 4 (2015)
Fergal J. Duffy, Marc Devocelle, David R. Croucher, Denis C. Shields
Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. BMC Bioinform. 15 (2014)
Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields, Catherine Mooney
CPPpred: prediction of cell penetrating peptides. Bioinform. 29 (23) (2013)
Kevin T. O'Brien, Niall J. Haslam, Denis C. Shields
SLiMScape: a protein short linear motif analysis plugin for Cytoscape. BMC Bioinform. 14 (2013)
Catherine Mooney, Niall J. Haslam, Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields
PeptideLocator: prediction of bioactive peptides in protein sequences. Bioinform. 29 (9) (2013)
Niall J. Haslam, Denis C. Shields
Profile-based short linear protein motif discovery. BMC Bioinform. 13 (2012)
Fergal P. Casey, Nevan J. Krogan, Denis C. Shields, Gerard Cagney
Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs. BMC Syst. Biol. 5 (2011)
Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards
SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Fergal J. Duffy, Mélanie Verniere, Marc Devocelle, Elise Bernard, Denis C. Shields, Anthony J. Chubb
CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids. J. Chem. Inf. Model. 51 (4) (2011)
Norman E. Davey, Richard J. Edwards, Denis C. Shields
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. BMC Bioinform. 11 (2010)
Praveen Surendran, Alice V. Stanton, Denis C. Shields
Genome wide association study of nonsynonymous Single Nucleotide Polymorphisms for seven common diseases. BMC Bioinform. 11 (S-10) (2010)
Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards
SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context. PRIB (2010)
Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards
SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Norman E. Davey, Denis C. Shields, Richard J. Edwards
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinform. 25 (4) (2009)
Fergal P. Casey, Emilie Pihan, Denis C. Shields
Discovery of Small Molecule Inhibitors of Protein-Protein Interactions Using Combined Ligand and Target Score Normalization. J. Chem. Inf. Model. 49 (12) (2009)
Fergal P. Casey, Gerard Cagney, Nevan J. Krogan, Denis C. Shields
Optimal stepwise experimental design for pairwise functional interaction studies. Bioinform. 24 (23) (2008)
Richard J. Edwards, Norman E. Davey, Denis C. Shields
CompariMotif: quick and easy comparisons of sequence motifs. Bioinform. 24 (10) (2008)
Fergal P. Casey, Norman E. Davey, Ivan Baran, Radka Svobodová Vareková, Denis C. Shields
Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO). J. Chem. Inf. Model. 48 (7) (2008)
Laavanya Parthasarathi, Fergal P. Casey, Amelie Stein, Patrick Aloy, Denis C. Shields
Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs. J. Chem. Inf. Model. 48 (10) (2008)
Norman E. Davey, Richard J. Edwards, Denis C. Shields
The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Ivan Baran, Radka Svobodová Vareková, Laavanya Parthasarathi, Simon Suchomel, Fergal P. Casey, Denis C. Shields
Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins. J. Chem. Inf. Model. 47 (2) (2007)
Laavanya Parthasarathi, Marc Devocelle, Chresten R. Søndergaard, Ivan Baran, Colm O'Dushlaine, Norman E. Davey, Richard J. Edwards, Niamh Moran, Dermot Kenny, Denis C. Shields
Absolute Net Charge and the Biological Activity of Oligopeptides. J. Chem. Inf. Model. 46 (5) (2006)
Richard J. Edwards, Denis C. Shields
BADASP: predicting functional specificity in protein families using ancestral sequences. Bioinform. 21 (22) (2005)
Richard J. Edwards, Denis C. Shields
GASP: Gapped Ancestral Sequence Prediction for proteins. BMC Bioinform. 5 (2004)
Itizar Frades, Richard J. Edwards, Denis C. Shields
Investigating the 3D Conformation of N-Terminally Constrained Oligopeptides. Spanish Bioinformatics Conference (2004)
Karsten Hokamp, Denis C. Shields, Kenneth H. Wolfe, Daniel R. Caffrey
Wrapping up BLAST and other applications for use on Unix clusters. Bioinform. 19 (3) (2003)
Philip J. Cotter, Daniel R. Caffrey, Denis C. Shields
Improved database searches for orthologous sequences by conditioning on outgroup sequences. Bioinform. 18 (1) (2002)
Cathal Seoighe, Denis C. Shields, Kenneth H. Wolfe
Genome duplication and the evolution of gene Order and chromosome number in yeast. German Conference on Bioinformatics (1997)
Denis C. Shields, Desmond G. Higgins, P. M. Sharp
GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content. Comput. Appl. Biosci. 8 (5) (1992)