PoPS: A Computational Tool for Modeling and Predicting Protease Specificity. - Sarah E. Boyd; Maria J. García de la Banda; Robert N. Pike; James C. Whisstock; George B. Rudy (CSB, 2004)

Progressive Multiple Alignment Using Sequence Triplet Optimizations and Three-residue Exchange Costs. - Arun Siddharth Konagurthu; James C. Whisstock; Peter J. Stuckey (J. Bioinform. Comput. Biol., 2004)

The REFOLD database: a tool for the optimization of protein expression and refolding. - Michelle K. M. Chow; Abdullah A. Amin; Kate F. Fulton; Thushan Fernando; Lawrence Kamau; Chris Batty; Michael Louca; Storm Ho; James C. Whisstock; Stephen P. Bottomley; Ashley M. Buckle (Nucleic Acids Res., 2006)

eResearch Solutions for High Throughput Structural Biology. - Noel G. Faux; Anthony Beitz; Mark A. Bate; Abdullah A. Amin; Ian Atkinson; Colin Enticott; Khalid Mahmood 001; Matthew Swift; Andrew E. Treloar; David Abramson 001; James C. Whisstock; Ashley M. Buckle (eScience, 2007)

High-throughput protein structure determination using grid computing. - Jason W. Schmidberger; Blair Bethwaite; Colin Enticott; Mark A. Bate; Steve G. Androulakis; Noel G. Faux; Cyril F. Reboul; Jennifer M. N. Phan; James C. Whisstock; Wojtek Goscinski; Slavisa Garic; David Abramson 001; et al. (IPDPS, 2009)

EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes. - Khalid Mahmood 001; Arun Siddharth Konagurthu; Jiangning Song; Ashley M. Buckle; Geoffrey I. Webb; James C. Whisstock (Bioinform., 2010)

Cascleave: towards more accurate prediction of caspase substrate cleavage sites. - Jiangning Song; Hao Tan; Hong-Bin Shen; Khalid Mahmood 001; Sarah E. Boyd; Geoffrey I. Webb; Tatsuya Akutsu; James C. Whisstock (Bioinform., 2010)

Automatic generation of protein structure cartoons with Pro-origami. - Alex D. Stivala; Michael Wybrow; Anthony Wirth; James C. Whisstock; Peter J. Stuckey (Bioinform., 2011)

Bioinformatic Approaches for Predicting substrates of Proteases. - Jiangning Song; Hao Tan; Sarah E. Boyd; Hong-Bin Shen; Khalid Mahmood 001; Geoffrey I. Webb; Tatsuya Akutsu; James C. Whisstock; Robert N. Pike (J. Bioinform. Comput. Biol., 2011)

Predicting giant transmembrane β-barrel architecture. - Cyril F. Reboul; Khalid Mahmood 001; James C. Whisstock; Michelle A. Dunstone (Bioinform., 2012)

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. - Mingjun Wang; Xing-Ming Zhao; Hao Tan; Tatsuya Akutsu; James C. Whisstock; Jiangning Song (Bioinform., 2014)

A New Model for Pore Formation by Cholesterol-Dependent Cytolysins. - Cyril F. Reboul; James C. Whisstock; Michelle A. Dunstone (PLoS Comput. Biol., 2014)

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome. - Fuyi Li; Chen Li 021; Mingjun Wang; Geoffrey I. Webb; Yang Zhang 010; James C. Whisstock; Jiangning Song (Bioinform., 2015)

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. - Fuyi Li; Yanan Wang 003; Chen Li 021; Tatiana T. Marquez-Lago; André Leier; Neil D. Rawlings; Gholamreza Haffari; Jerico Nico De Leon Revote; Tatsuya Akutsu; Kuo-Chen Chou; Anthony W. Purcell; Robert N. Pike; et al. (Briefings Bioinform., 2019)

Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learning. - Ying Xu; André Leier; Tatiana T. Marquez-Lago; Jue Xie; Antonio Jimeno-Yepes; James C. Whisstock; Campbell Wilson; Jiangning Song (AMIA, 2020)

PhosTransfer: A Deep Transfer Learning Framework for Kinase-Specific Phosphorylation Site Prediction in Hierarchy. - Ying Xu; Campbell Wilson; André Leier; Tatiana T. Marquez-Lago; James C. Whisstock; Jiangning Song (PAKDD (2), 2020)

Juno: a Python-based graphical package for optical system design. - David Dierickx; Patrick Cleeve; Sergey Gorelick; James C. Whisstock; Alex De Marco (CoRR, 2022)

Mining folded proteomes in the era of accurate structure prediction. - Charles Bayly-Jones; James C. Whisstock (PLoS Comput. Biol., 2022)