Denis C. Shields

According to our database, Denis C. Shields authored at least 33 papers between 1992 and 2021.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2021

Computational modelling of chromosomally clustering protein domains in bacteria.

Chiara E. Cotroneo, Isobel Claire Gormley, Denis C. Shields, Michael Salter-Townshend

BMC Bioinform., 2021

2016

ProViz - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences.

Peter Jehl, Jean Manguy, Denis C. Shields, Desmond G. Higgins, Norman E. Davey

Nucleic Acids Res., 2016

2015

Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies.

Federica Lombardi, Kalyan Golla, Darren J. Fitzpatrick, Fergal P. Casey, Niamh Moran, Denis C. Shields

PLoS Comput. Biol., 2015

Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals Protein Interfaces Readily Targetable by Cyclic Peptides.

Fergal J. Duffy, Darragh O'Donovan, Marc Devocelle, Niamh Moran, David J. O'Connell, Denis C. Shields

J. Chem. Inf. Model., 2015

SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks.

Emily Olorin, Kevin T. O'Brien, Nicolas Palopoli, Åsa Pérez-Bercoff, Denis C. Shields, Richard J. Edwards

F1000Research, 2015

2014

Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions.

Fergal J. Duffy, Marc Devocelle, David R. Croucher, Denis C. Shields

BMC Bioinform., 2014

2013

SLiMScape: a protein short linear motif analysis plugin for Cytoscape.

Kevin T. O'Brien, Niall J. Haslam, Denis C. Shields

BMC Bioinform., 2013

PeptideLocator: prediction of bioactive peptides in protein sequences.

Catherine Mooney, Niall J. Haslam, Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields

Bioinform., 2013

CPPpred: prediction of cell penetrating peptides.

Thérèse A. Holton, Gianluca Pollastri, Denis C. Shields, Catherine Mooney

Bioinform., 2013

2012

Profile-based short linear protein motif discovery.

Niall J. Haslam, Denis C. Shields

BMC Bioinform., 2012

2011

SLiMSearch 2.0: biological context for short linear motifs in proteins.

Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards

Nucleic Acids Res., 2011

CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids.

Fergal J. Duffy, Mélanie Verniere, Marc Devocelle, Elise Bernard, Denis C. Shields, Anthony J. Chubb

J. Chem. Inf. Model., 2011

Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs.

Fergal P. Casey, Nevan J. Krogan, Denis C. Shields, Gerard Cagney

BMC Syst. Biol., 2011

2010

SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs.

Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards

Nucleic Acids Res., 2010

Genome wide association study of nonsynonymous Single Nucleotide Polymorphisms for seven common diseases.

Praveen Surendran, Alice V. Stanton, Denis C. Shields

BMC Bioinform., 2010

Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins.

Norman E. Davey, Richard J. Edwards, Denis C. Shields

BMC Bioinform., 2010

SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context.

Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards

Proceedings of the Pattern Recognition in Bioinformatics, 2010

2009

Discovery of Small Molecule Inhibitors of Protein-Protein Interactions Using Combined Ligand and Target Score Normalization.

Fergal P. Casey, Emilie Pihan, Denis C. Shields

J. Chem. Inf. Model., 2009

Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery.

Norman E. Davey, Denis C. Shields, Richard J. Edwards

Bioinform., 2009

2008

Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs.

Laavanya Parthasarathi, Fergal P. Casey, Amelie Stein, Patrick Aloy, Denis C. Shields

J. Chem. Inf. Model., 2008

Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO).

Fergal P. Casey, Norman E. Davey, Ivan Baran, Radka Svobodová Vareková, Denis C. Shields

J. Chem. Inf. Model., 2008

CompariMotif: quick and easy comparisons of sequence motifs.

Richard J. Edwards, Norman E. Davey, Denis C. Shields

Bioinform., 2008

Optimal stepwise experimental design for pairwise functional interaction studies.

Fergal P. Casey, Gerard Cagney, Nevan J. Krogan, Denis C. Shields

Bioinform., 2008

2007

The SLiMDisc server: short, linear motif discovery in proteins.

Norman E. Davey, Richard J. Edwards, Denis C. Shields

Nucleic Acids Res., 2007

Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins.

Ivan Baran, Radka Svobodová Vareková, Laavanya Parthasarathi, Simon Suchomel, Fergal P. Casey, Denis C. Shields

J. Chem. Inf. Model., 2007

2006

Absolute Net Charge and the Biological Activity of Oligopeptides.

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

J. Chem. Inf. Model., 2006

2005

BADASP: predicting functional specificity in protein families using ancestral sequences.

Richard J. Edwards, Denis C. Shields

Bioinform., 2005

2004

GASP: Gapped Ancestral Sequence Prediction for proteins.

Richard J. Edwards, Denis C. Shields

BMC Bioinform., 2004

Investigating the 3D Conformation of N-Terminally Constrained Oligopeptides.

Itizar Frades, Richard J. Edwards, Denis C. Shields

Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004

2003

Wrapping up BLAST and other applications for use on Unix clusters.

Karsten Hokamp, Denis C. Shields, Kenneth H. Wolfe, Daniel R. Caffrey

Bioinform., 2003

2002

Improved database searches for orthologous sequences by conditioning on outgroup sequences.

Philip J. Cotter, Daniel R. Caffrey, Denis C. Shields

Bioinform., 2002

1997

Genome duplication and the evolution of gene Order and chromosome number in yeast.

Cathal Seoighe, Denis C. Shields, Kenneth H. Wolfe

Proceedings of the German Conference on Bioinformatics, 1997

1992

GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content.

Denis C. Shields, Desmond G. Higgins, P. M. Sharp

Comput. Appl. Biosci., 1992