Jonathan D. Hirst

Orcid: 0000-0002-2726-0983

According to our database1, Jonathan D. Hirst authored at least 48 papers between 1994 and 2024.

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Bibliography

2024
Solvent flashcards: a visualisation tool for sustainable chemistry.
J. Cheminformatics, December, 2024

Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations.
J. Chem. Inf. Model., January, 2024

Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors.
J. Chem. Inf. Model., 2024

Three-Branch Molecular Representation Learning Framework for Predicting Molecular Properties in Drug Discovery.
Proceedings of the 48th IEEE Annual Computers, Software, and Applications Conference, 2024

2023
AI4Green: An Open-Source ELN for Green and Sustainable Chemistry.
J. Chem. Inf. Model., May, 2023

2022
Kernel Methods for Predicting Yields of Chemical Reactions.
J. Chem. Inf. Model., 2022

Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4.
J. Chem. Inf. Model., 2022

Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis.
J. Chem. Inf. Model., 2022

2020
Molecular Simulation of αvβ6 Integrin Inhibitors.
J. Chem. Inf. Model., 2020

2017
Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin.
J. Comput. Chem., 2017

Computing infrared spectra of proteins using the exciton model.
J. Comput. Chem., 2017

Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III.
J. Comput. Chem., 2017

2011
Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain.
J. Cheminformatics, 2011

Water order profiles on phospholipid/cholesterol membrane bilayer surfaces.
J. Comput. Chem., 2011

2010
Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin.
J. Comput. Aided Mol. Des., 2010

A learning classifier system with mutual-information-based fitness.
Evol. Intell., 2010

Predicting <i>beta</i>-turns and their types using predicted backbone dihedral angles and secondary structures.
BMC Bioinform., 2010

Automatic structure classification of small proteins using random forest.
BMC Bioinform., 2010

2009
Prediction of topological contacts in proteins using learning classifier systems.
Soft Comput., 2009

Interpretable correlation descriptors for quantitative structure-activity relationships.
J. Cheminformatics, 2009

Supervised machine learning algorithms for protein structure classification.
Comput. Biol. Chem., 2009

Prediction of backbone dihedral angles and protein secondary structure using support vector machines.
BMC Bioinform., 2009

Automated Alphabet Reduction for Protein Datasets.
BMC Bioinform., 2009

DichroCalc - circular and linear dichroism online.
Bioinform., 2009

2008
Data Mining in Proteomics with Learning Classifier Systems.
Proceedings of the Learning Classifier Systems in Data Mining, 2008

Prediction of glycosylation sites using random forests.
BMC Bioinform., 2008

Prediction of recursive convex hull class assignments for protein residues.
Bioinform., 2008

2007
Similarity by Compression.
J. Chem. Inf. Model., 2007

TMACC: Interpretable Correlation Descriptors for Quantitative Structure-Activity Relationships.
J. Chem. Inf. Model., 2007

Contemporary QSAR Classifiers Compared.
J. Chem. Inf. Model., 2007

ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information.
BMC Bioinform., 2007

Automated alphabet reduction method with evolutionary algorithms for protein structure prediction.
Proceedings of the Genetic and Evolutionary Computation Conference, 2007

2006
Coordination number prediction using learning classifier systems: performance and interpretability.
Proceedings of the Genetic and Evolutionary Computation Conference, 2006

From HP Lattice Models to Real Proteins: Coordination Number Prediction Using Learning Classifier Systems.
Proceedings of the Applications of Evolutionary Computing, 2006

2005
Exploring Phase-Transfer Catalysis with Molecular Dynamics and 3D/4D Quantitative Structure-Selectivity Relationships.
J. Chem. Inf. Model., 2005

Inhibition of the Tyrosine Kinase, Syk, Analyzed by Stepwise Nonparametric Regression.
J. Chem. Inf. Model., 2005

Lattice models of peptide aggregation: Evaluation of conformational search algorithms.
J. Comput. Chem., 2005

A fuzzy sets based generalization of contact maps for the overlap of protein structures.
Fuzzy Sets Syst., 2005

2004
On the Stability of CoMFA Models.
J. Chem. Inf. Model., 2004

Predicting protein secondary structure by cascade-correlation neural networks.
Bioinform., 2004

Recent Applications of Neural Networks in Bioinformatics.
Proceedings of the Biological and Artificial Intelligence Environments, 2004

2002
Multimeme Algorithms for Protein Structure Prediction.
Proceedings of the Parallel Problem Solving from Nature, 2002

Alignment Of Protein Structures With A Memetic Evolutionary Algorithm.
Proceedings of the GECCO 2002: Proceedings of the Genetic and Evolutionary Computation Conference, 2002

2000
Nonparametric Regression Applied to Quantitative Structure-Activity Relationships.
J. Chem. Inf. Comput. Sci., 2000

1998
Assessing energy functions for flexible docking.
J. Comput. Chem., 1998

Assessing search strategies for flexible docking.
J. Comput. Chem., 1998

1994
Quantitative structure-activity relationships by neural networks and inductive logic programming. II. The inhibition of dihydrofolate reductase by triazines.
J. Comput. Aided Mol. Des., 1994

Quantitative structure-activity relationships by neural networks and inductive logic programming. I. The inhibition of dihydrofolate reductase by pyrimidines.
J. Comput. Aided Mol. Des., 1994


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