List of works - Jonathan D. Hirst

A Machine Learning Protocol for Predicting Protein Infrared Spectra

scientific article published on 30 October 2020

A sequential molecular mechanics/quantum mechanics study of the electronic spectra of amides.

scientific article published in October 2004

Accelerating electrostatic pair methods on graphical processing units to study molecules in supercritical carbon dioxide

scientific article published on 2 June 2014

Application of non-parametric regression to quantitative structure-activity relationships.

scientific article published on April 2002

Assembly pathway of a designed alpha-helical protein fiber.

scientific article

Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica

scientific article published on 15 November 2018

Automated alphabet reduction for protein datasets.

scientific article

Automatic structure classification of small proteins using random forest.

scientific article

Calculating the fluorescence of 5-hydroxytryptophan in proteins.

scientific article

Calculation of partition functions and free energies of a binary mixture using the energy partitioning method: application to carbon dioxide and methane

scientific article published on 6 April 2012

Calculations of protein circular dichroism from first principles.

scientific article published in May 2004

Calculations on the electronic excited states of ureas and oligoureas

scientific article published on 03 March 2007

Charge-transfer transitions in protein circular dichroism calculations

scientific article published in September 2006

Charge-transfer transitions in the vacuum-ultraviolet of protein circular dichroism spectra

scientific article published on 17 January 2008

Circular and linear dichroism of proteins.

scientific article published on 20 February 2007

Conformation and dynamics of the three-helix bundle UBA domain of p62 from experiment and simulation

scientific article

Contemporary QSAR classifiers compared.

scientific article

Cooperativity and site selectivity in the ileal lipid binding protein

scientific article published on 25 June 2013

Di-8-ANEPPS emission spectra in phospholipid/cholesterol membranes: a theoretical study

scientific article published on 22 March 2011

DichroCalc--circular and linear dichroism online

scientific article

Do active site conformations of small ligands correspond to low free-energy solution structures?

scientific article published on 01 November 1998

Dynamics of chemical bond: general discussion

scientific article published on 01 January 2015

Effects of ulapualide A and synthetic macrolide analogues on actin dynamics and gene regulation.

scientific article published on February 2007

Electronic structure and circular dichroism spectroscopy of naphthalenediimide nanotubes.

scientific article

Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis

scientific article published on 16 October 2017

Exploring phase-transfer catalysis with molecular dynamics and 3D/4D quantitative structure-selectivity relationships

scientific article published in July 2005

Exploring protein structural dissimilarity to facilitate structure classification

scientific article published on 19 September 2009

First principles predictions of thermophysical properties of refrigerant mixtures

scientific article published in March 2011

First-principles calculations of protein circular dichroism in the far-ultraviolet and beyond.

scientific article

First-principles calculations of protein circular dichroism in the near ultraviolet.

scientific article

Flow linear dichroism of some prototypical proteins.

scientific article published in September 2009

Gibbs ensemble Monte Carlo simulations of binary mixtures of methane, difluoromethane, and carbon dioxide

scientific article published in March 2010

Helicity, circular dichroism and molecular dynamics of proteins

scientific article published on 01 October 1994

Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra

scientific article published on 25 July 2019

Inhibition of the tyrosine kinase, Syk, analyzed by stepwise nonparametric regression

scientific article published in May 2005

Interpretable correlation descriptors for quantitativestructure-activity relationships

scientific article (publication date: 24 December 2009)

Lattice models of peptide aggregation: evaluation of conformational search algorithms.

scientific article published in November 2005

Local and Global Dynamics: general discussion

scientific article published on 01 January 2015

Machine learning in virtual screening.

scientific article published on May 2009

Microscopic structure of liquid 1-1-1-2-tetrafluoroethane (R134a) from Monte Carlo simulation

scientific article published on 7 September 2010

Modeling the Absorption Spectrum of Tryptophan in Proteins

scientific article published in December 2005

Modeling the amide I bands of small peptides

scientific article published on 01 July 2006

Modeling the infrared and circular dichroism spectroscopy of a bridged cyclic diamide

scientific article published on 23 February 2011

Molecular Dynamics Simulations Using Graphics Processing Units.

scientific article

Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin

scientific article published on 5 November 2009

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

scientific article

Molecular dynamics simulations of isolated helices of myoglobin

scientific article published in June 1995

Molecular simulation of the binary mixture of 1-1-1-2-tetrafluoroethane and carbon dioxide

scientific article

Molecular simulations and visualization: introduction and overview

scientific article published on 6 October 2014

Nonlinear quantitative structure-activity relationship for the inhibition of dihydrofolate reductase by pyrimidines.

scientific article published in August 1996

Nonparametric regression applied to quantitative structure-activity relationships

scientific article published on March 2000

On the stability of CoMFA models

scientific article published on 01 July 2004

Population dynamics simulations of functional model proteins

scientific article published in October 2005

Predicting protein secondary structure by cascade-correlation neural networks

scientific article published on 22 January 2004

Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures ⬇️

scientific article published on July 31, 2010

Prediction of backbone dihedral angles and protein secondary structure using support vector machines

scientific article

Prediction of glycosylation sites using random forests

scientific article

Prediction of recursive convex hull class assignments for protein residues.

scientific article

ProCKSI: a decision support system for Protein (structure) Comparison, Knowledge, Similarity and Information

scientific article

Protein secondary structure prediction with dihedral angles

scientific article published on 01 May 2005

Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet

scientific article

Quantitative structure-activity relationships by neural networks and inductive logic programming. I. The inhibition of dihydrofolate reductase by pyrimidines.

scientific article published in August 1994

Quantitative structure-activity relationships by neural networks and inductive logic programming. II. The inhibition of dihydrofolate reductase by triazines

scientific article published in August 1994

Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin.

scientific article published on April 2017

Rapid calculation of partition functions and free energies of fluids

scientific article published in November 2011

Short Hydrogen Bonds, Circular Dichroism, and Over-Estimates of Peptide Helicity We thank BBSRC for financial support (grant 42/B1524)

Similarity by compression

scientific article published in January 2007

Stabilizing interactions between aromatic and basic side chains in alpha-helical peptides and proteins. Tyrosine effects on helix circular dichroism

scientific article published in October 2002

Statistical analysis of unlabeled point sets: comparing molecules in chemoinformatics

scientific article published in March 2007

Stereoselective disulfide formation stabilizes the local peptide conformation in nisin mimics

scientific article published on November 2010

Structural insights into the two sequential folding transition states of the PB1 domain of NBR1 from Φ value analysis and biased molecular dynamics simulations

scientific article published on 8 December 2010

Studying biomacromolecules with two-dimensional infrared spectroscopy

scientific article published in January 2013

Supervised machine learning algorithms for protein structure classification.

scientific article

TMACC: interpretable correlation descriptors for quantitative structure-activity relationships.

scientific article published on March 2007

The JMGM/MGMS graphics prize

scientific article

The evolutionary landscape of functional model proteins

scientific article published on 01 September 1999

The structural determinants of macrolide-actin binding: in silico insights.

scientific article published on 9 March 2007

Theoretical studies of time-resolved spectroscopy of protein folding

scientific article published in January 2003

Time and Space resolved Methods: general discussion

scientific article

Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization

scientific article published on 01 September 2019

Topical perspectives

scientific article published on 22 July 2010

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

scientific article published on 29 June 2020

Vibronic structure in the far-UV electronic circular dichroism spectra of proteins

scientific article published on 01 January 2015

Water order profiles on phospholipid/cholesterol membrane bilayer surfaces

scientific article published on 01 June 2011

List of works by Jonathan D. Hirst

A Machine Learning Protocol for Predicting Protein Infrared Spectra

A sequential molecular mechanics/quantum mechanics study of the electronic spectra of amides.

Accelerating electrostatic pair methods on graphical processing units to study molecules in supercritical carbon dioxide

Application of non-parametric regression to quantitative structure-activity relationships.

Assembly pathway of a designed alpha-helical protein fiber.

Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica

Automated alphabet reduction for protein datasets.

Automatic structure classification of small proteins using random forest.

Calculating the fluorescence of 5-hydroxytryptophan in proteins.

Calculation of partition functions and free energies of a binary mixture using the energy partitioning method: application to carbon dioxide and methane

Calculations of protein circular dichroism from first principles.

Calculations on the electronic excited states of ureas and oligoureas

Charge-transfer transitions in protein circular dichroism calculations

Charge-transfer transitions in the vacuum-ultraviolet of protein circular dichroism spectra

Circular and linear dichroism of proteins.

Conformation and dynamics of the three-helix bundle UBA domain of p62 from experiment and simulation

Contemporary QSAR classifiers compared.

Cooperativity and site selectivity in the ileal lipid binding protein

Di-8-ANEPPS emission spectra in phospholipid/cholesterol membranes: a theoretical study

DichroCalc--circular and linear dichroism online

Do active site conformations of small ligands correspond to low free-energy solution structures?

Dynamics of chemical bond: general discussion

Effects of ulapualide A and synthetic macrolide analogues on actin dynamics and gene regulation.

Electronic structure and circular dichroism spectroscopy of naphthalenediimide nanotubes.

Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis

Exploring phase-transfer catalysis with molecular dynamics and 3D/4D quantitative structure-selectivity relationships

Exploring protein structural dissimilarity to facilitate structure classification

First principles predictions of thermophysical properties of refrigerant mixtures

First-principles calculations of protein circular dichroism in the far-ultraviolet and beyond.

First-principles calculations of protein circular dichroism in the near ultraviolet.

Flow linear dichroism of some prototypical proteins.

Gibbs ensemble Monte Carlo simulations of binary mixtures of methane, difluoromethane, and carbon dioxide

Helicity, circular dichroism and molecular dynamics of proteins

Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra

Inhibition of the tyrosine kinase, Syk, analyzed by stepwise nonparametric regression

Interpretable correlation descriptors for quantitativestructure-activity relationships

Lattice models of peptide aggregation: evaluation of conformational search algorithms.

Local and Global Dynamics: general discussion

Machine learning in virtual screening.

Microscopic structure of liquid 1-1-1-2-tetrafluoroethane (R134a) from Monte Carlo simulation

Modeling the Absorption Spectrum of Tryptophan in Proteins

Modeling the amide I bands of small peptides

Modeling the infrared and circular dichroism spectroscopy of a bridged cyclic diamide

Molecular Dynamics Simulations Using Graphics Processing Units.

Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin

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

Molecular dynamics simulations of isolated helices of myoglobin

Molecular simulation of the binary mixture of 1-1-1-2-tetrafluoroethane and carbon dioxide

Molecular simulations and visualization: introduction and overview

Nonlinear quantitative structure-activity relationship for the inhibition of dihydrofolate reductase by pyrimidines.

Nonparametric regression applied to quantitative structure-activity relationships

On the stability of CoMFA models

Population dynamics simulations of functional model proteins

Predicting protein secondary structure by cascade-correlation neural networks

Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures ⬇️

Prediction of backbone dihedral angles and protein secondary structure using support vector machines

Prediction of glycosylation sites using random forests

Prediction of recursive convex hull class assignments for protein residues.

ProCKSI: a decision support system for Protein (structure) Comparison, Knowledge, Similarity and Information

Protein secondary structure prediction with dihedral angles

Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet

Quantitative structure-activity relationships by neural networks and inductive logic programming. I. The inhibition of dihydrofolate reductase by pyrimidines.

Quantitative structure-activity relationships by neural networks and inductive logic programming. II. The inhibition of dihydrofolate reductase by triazines

Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin.

Rapid calculation of partition functions and free energies of fluids

Short Hydrogen Bonds, Circular Dichroism, and Over-Estimates of Peptide Helicity We thank BBSRC for financial support (grant 42/B1524)

Similarity by compression

Stabilizing interactions between aromatic and basic side chains in alpha-helical peptides and proteins. Tyrosine effects on helix circular dichroism

Statistical analysis of unlabeled point sets: comparing molecules in chemoinformatics

Stereoselective disulfide formation stabilizes the local peptide conformation in nisin mimics

Structural insights into the two sequential folding transition states of the PB1 domain of NBR1 from Φ value analysis and biased molecular dynamics simulations

Studying biomacromolecules with two-dimensional infrared spectroscopy

Supervised machine learning algorithms for protein structure classification.

TMACC: interpretable correlation descriptors for quantitative structure-activity relationships.

The JMGM/MGMS graphics prize

The evolutionary landscape of functional model proteins

The structural determinants of macrolide-actin binding: in silico insights.

Theoretical studies of time-resolved spectroscopy of protein folding

Time and Space resolved Methods: general discussion