Quantitative structure-activity relationships by neural networks and inductive logic programming. I. The inhibition of dihydrofolate reductase by pyrimidines. - Jonathan D. Hirst; Ross D. King; Michael J. E. Sternberg (J. Comput. Aided Mol. Des., 1994)

Quantitative structure-activity relationships by neural networks and inductive logic programming. II. The inhibition of dihydrofolate reductase by triazines. - Jonathan D. Hirst; Ross D. King; Michael J. E. Sternberg (J. Comput. Aided Mol. Des., 1994)

Assessing search strategies for flexible docking. - Michal Vieth; Jonathan D. Hirst; Brian N. Dominy; Heidi Daigler; Charles L. Brooks III (J. Comput. Chem., 1998)

Assessing energy functions for flexible docking. - Michal Vieth; Jonathan D. Hirst; Andrzej Kolinski; Charles L. Brooks III (J. Comput. Chem., 1998)

Nonparametric Regression Applied to Quantitative Structure-Activity Relationships. - Pere Constans; Jonathan D. Hirst (J. Chem. Inf. Comput. Sci., 2000)

Alignment Of Protein Structures With A Memetic Evolutionary Algorithm. - Robert D. Carr; William E. Hart; Natalio Krasnogor; Jonathan D. Hirst; Edmund K. Burke; James Smith (GECCO, 2002)

Multimeme Algorithms for Protein Structure Prediction. - Natalio Krasnogor; B. P. Blackburne; Edmund K. Burke; Jonathan D. Hirst (PPSN, 2002)

Recent Applications of Neural Networks in Bioinformatics. - Matthew J. Wood; Jonathan D. Hirst (WIRN, 2004)

Predicting protein secondary structure by cascade-correlation neural networks. - Matthew J. Wood; Jonathan D. Hirst (Bioinform., 2004)

On the Stability of CoMFA Models. - James L. Melville; Jonathan D. Hirst (J. Chem. Inf. Model., 2004)

A fuzzy sets based generalization of contact maps for the overlap of protein structures. - David A. Pelta; Natalio Krasnogor; Carlos Bousoño-Calzón; José L. Verdegay; Jonathan D. Hirst; Edmund K. Burke (Fuzzy Sets Syst., 2005)

Lattice models of peptide aggregation: Evaluation of conformational search algorithms. - Mark T. Oakley; Jonathan M. Garibaldi; Jonathan D. Hirst (J. Comput. Chem., 2005)

Inhibition of the Tyrosine Kinase, Syk, Analyzed by Stepwise Nonparametric Regression. - T. John McNeany; Jonathan D. Hirst (J. Chem. Inf. Model., 2005)

Exploring Phase-Transfer Catalysis with Molecular Dynamics and 3D/4D Quantitative Structure-Selectivity Relationships. - James L. Melville; Kevin R. J. Lovelock; Claire Wilson; Bryan Allbutt; Edmund K. Burke; Barry Lygo; Jonathan D. Hirst (J. Chem. Inf. Model., 2005)

From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems. - Michael Stout; Jaume Bacardit; Jonathan D. Hirst; Natalio Krasnogor; Jacek Blazewicz (EvoWorkshops, 2006)

Coordination number prediction using learning classifier systems: performance and interpretability. - Jaume Bacardit; Michael Stout; Natalio Krasnogor; Jonathan D. Hirst; Jacek Blazewicz (GECCO, 2006)

Automated alphabet reduction method with evolutionary algorithms for protein structure prediction. - Jaume Bacardit; Michael Stout; Jonathan D. Hirst; Kumara Sastry; Xavier Llorà; Natalio Krasnogor (GECCO, 2007)

ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information. - Daniel Barthel; Jonathan D. Hirst; Jacek Blazewicz; Edmund K. Burke; Natalio Krasnogor (BMC Bioinform., 2007)

Contemporary QSAR Classifiers Compared. - Craig L. Bruce; James L. Melville; Stephen D. Pickett; Jonathan D. Hirst (J. Chem. Inf. Model., 2007)

TMACC: Interpretable Correlation Descriptors for Quantitative Structure-Activity Relationships. - James L. Melville; Jonathan D. Hirst (J. Chem. Inf. Model., 2007)

Similarity by Compression. - James L. Melville; Jenna F. Riley; Jonathan D. Hirst (J. Chem. Inf. Model., 2007)

Prediction of recursive convex hull class assignments for protein residues. - Michael Stout; Jaume Bacardit; Jonathan D. Hirst; Natalio Krasnogor (Bioinform., 2008)

Prediction of glycosylation sites using random forests. - Stephen E. Hamby; Jonathan D. Hirst (BMC Bioinform., 2008)

Data Mining in Proteomics with Learning Classifier Systems. - Jaume Bacardit; Michael Stout; Jonathan D. Hirst; Natalio Krasnogor (Learning Classifier Systems in Data Mining, 2008)

DichroCalc - circular and linear dichroism online. - Benjamin M. Bulheller; Jonathan D. Hirst (Bioinform., 2009)

Automated Alphabet Reduction for Protein Datasets. - Jaume Bacardit; Michael Stout; Jonathan D. Hirst; Alfonso Valencia; Robert Elliott Smith; Natalio Krasnogor (BMC Bioinform., 2009)

Prediction of backbone dihedral angles and protein secondary structure using support vector machines. - Petros Kountouris; Jonathan D. Hirst (BMC Bioinform., 2009)

Supervised machine learning algorithms for protein structure classification. - Pooja Jain; Jonathan M. Garibaldi; Jonathan D. Hirst (Comput. Biol. Chem., 2009)

Interpretable correlation descriptors for quantitative structure-activity relationships. - Benson M. Spowage; Craig L. Bruce; Jonathan D. Hirst (J. Cheminformatics, 2009)

Prediction of topological contacts in proteins using learning classifier systems. - Michael Stout; Jaume Bacardit; Jonathan D. Hirst; Robert Elliott Smith; Natalio Krasnogor (Soft Comput., 2009)

Automatic structure classification of small proteins using random forest. - Pooja Jain; Jonathan D. Hirst (BMC Bioinform., 2010)

Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures. - Petros Kountouris; Jonathan D. Hirst (BMC Bioinform., 2010)

A learning classifier system with mutual-information-based fitness. - Robert Elliott Smith; Max Kun Jiang; Jaume Bacardit; Michael Stout; Natalio Krasnogor; Jonathan D. Hirst (Evol. Intell., 2010)

Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin. - Abrar Hussain; James L. Melville; Jonathan D. Hirst (J. Comput. Aided Mol. Des., 2010)

Water order profiles on phospholipid/cholesterol membrane bilayer surfaces. - David Robinson; Nicholas A. Besley; Paul O'shea; Jonathan D. Hirst (J. Comput. Chem., 2011)

Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain. - Abrar Hussain; Peter E. Shaw; Jonathan D. Hirst (J. Cheminformatics, 2011)

Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III. - Jonathan D. Hirst; Wonpil Im; Joan-Emma Shea (J. Comput. Chem., 2017)

Computing infrared spectra of proteins using the exciton model. - Fouad S. Husseini; David Robinson; Neil T. Hunt; Anthony W. Parker; Jonathan D. Hirst (J. Comput. Chem., 2017)

Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin. - Christian J. Suess; Jonathan D. Hirst; Nicholas A. Besley (J. Comput. Chem., 2017)

Molecular Simulation of αvβ6 Integrin Inhibitors. - Ellen E. Guest; Steven A. Oatley; Simon J. F. Macdonald; Jonathan D. Hirst (J. Chem. Inf. Model., 2020)

Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis. - Samuel J. H. Gaughan; Jonathan D. Hirst; Anna K. Croft; Christof M. Jäger (J. Chem. Inf. Model., 2022)

Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. - Ellen E. Guest; Luis F. Cervantes; Stephen D. Pickett; Charles L. Brooks III; Jonathan D. Hirst (J. Chem. Inf. Model., 2022)

Kernel Methods for Predicting Yields of Chemical Reactions. - Alexe L. Haywood; Joseph Redshaw; Magnus W. D. Hanson-Heine; Adam Taylor; Alex Brown; Andrew M. Mason; Thomas Gärtner 001; Jonathan D. Hirst (J. Chem. Inf. Model., 2022)

AI4Green: An Open-Source ELN for Green and Sustainable Chemistry. - Samuel Boobier; Joseph C. Davies; Ivan N. Derbenev; Christopher M. Handley; Jonathan D. Hirst (J. Chem. Inf. Model., 2023)

Three-Branch Molecular Representation Learning Framework for Predicting Molecular Properties in Drug Discovery. - Yu Liu; Lihui Duo; Jonathan D. Hirst; Jianfeng Ren; Bencan Tang; Dave Towey (COMPSAC, 2024)

Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors. - Shayantan Chaudhuri; David M. Rogers 002; Christopher J. Hayes; Katherine Inzani; Jonathan D. Hirst (J. Chem. Inf. Model., 2024)

Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations. - Toby E. King; James R. Humphrey; Charles A. Laughton; Neil R. Thomas; Jonathan D. Hirst (J. Chem. Inf. Model., 2024)

Solvent flashcards: a visualisation tool for sustainable chemistry. - Joseph Heeley; Samuel Boobier; Jonathan D. Hirst (J. Cheminformatics, 2024)

Chemically-aware Attention-based Multi-modal Fusion Framework for Molecular Representation Learning. - Yu Liu; Jonathan D. Hirst; Jianfeng Ren; Bencan Tang; Dave Towey (COMPSAC, 2025)

Enhancing Monte Carlo Tree Search for Retrosynthesis. - Ton M. Blackshaw; Joseph C. Davies; Kristian T. Spoerer; Jonathan D. Hirst (J. Chem. Inf. Model., 2025)