All Outputs (60)

Electronic Circular Dichroism Spectroscopy of Proteins (2019)
Journal Article
Rogers, D. M., Jasim, S. B., Dyer, N. T., Auvray, F., Réfrégiers, M., & Hirst, J. D. (2019). Electronic Circular Dichroism Spectroscopy of Proteins. Chem, 5(11), 2751-2774. https://doi.org/10.1016/j.chempr.2019.07.008

Circular dichroism (CD) is an important spectroscopic technique that enables the characterization of protein secondary and tertiary structure. Proteins can undergo changes in their structure when they participate in processes, for example, ligand bin... Read More about Electronic Circular Dichroism Spectroscopy of Proteins.

Active search for computer-aided drug design (2018)
Journal Article
Oglic, D., Oatley, S. A., Macdonald, S. J., McInally, T., Garnett, R., Hirst, J. D., & Gärtner, T. (in press). Active search for computer-aided drug design. Molecular Informatics, 37, https://doi.org/10.1002/minf.201700130

We consider lead discovery as active search in a space of labelled graphs. In particular, we extend our recent data-driven adaptive Markov chain approach, and evaluate it on a focused drug design problem, where we search for an antagonist of an av in... Read More about Active search for computer-aided drug design.

DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet (2017)
Journal Article
Jasim, S. B., Li, Z., Guest, E. E., & Hirst, J. D. (in press). DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet. Journal of Molecular Biology, https://doi.org/10.1016/j.jmb.2017.12.009

A fully quantitative theory connecting protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. The web-server DichroCalc (http://comp.chem.nottingham.ac.u... Read More about DichroCalc: improvements in computing protein circular dichroism spectroscopy in the near-ultraviolet.

Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis (2017)
Journal Article
Shaw, D., Hill, R., Simpson, N., Husseini, F., Robb, K., Greetham, G. M., …Hunt, N. (in press). Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis. Chemical Science, 8, https://doi.org/10.1039/C7SC03336B

Antimicrobial resistance represents a growing global health problem. The emergence of novel resistance mechanisms necessitates the development of alternative approaches to investigate the molecular fundamentals of resistance, leading ultimately to ne... Read More about Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis.

Quantum chemical calculations of tryptophan?heme electron and excitation energy transfer rates in myoglobin (2017)
Journal Article
Suess, C. J., Hirst, J. D., & Besley, N. A. (2017). Quantum chemical calculations of tryptophan?heme electron and excitation energy transfer rates in myoglobin. Journal of Computational Chemistry, 38(17), 1495-1502. https://doi.org/10.1002/jcc.24793

The development of optical multidimensional spectroscopic techniques has opened up new possibilities for the study of biological processes. Recently, ultrafast two- dimensional ultraviolet spectroscopy experiments have determined the rates of tryptop... Read More about Quantum chemical calculations of tryptophan?heme electron and excitation energy transfer rates in myoglobin.

Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet (2017)
Journal Article
Li, Z., & Hirst, J. D. (in press). Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet. RSC Advances, https://doi.org/10.1039/C7SC00586E

Vibrational structure in the near-UV circular dichroism (CD) spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. A fully quantitative theory of the relationship betwee... Read More about Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet.

Computing infrared spectra of proteins using the exciton model (2016)
Journal Article
Husseini, F. S., Robinson, D., Hunt, N. T., Parker, A. W., & Hirst, J. (in press). Computing infrared spectra of proteins using the exciton model. Journal of Computational Chemistry, 38(16), https://doi.org/10.1002/jcc.24674

The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are... Read More about Computing infrared spectra of proteins using the exciton model.

Probing polyoxometalate-protein interactions using molecular dynamics simulations (2016)
Journal Article
Solé-Daura, A., Goovaerts, V., Stroobants, K., Absillis, G., Jiménez-Lozano, P., Poblet, J. M., …Carbó, J. J. (2016). Probing polyoxometalate-protein interactions using molecular dynamics simulations. Chemistry - A European Journal, 22(43), 15280-15289. https://doi.org/10.1002/chem.201602263

The molecular interactions between the Ce(IV)-substituted Keggin anion [PW11O39Ce(OH2)4]3- (CeK) and hen egg white lysozyme (HEWL), was investigated by molecular dynamics (MD) simulations. We compared the analysis of CeK with the Ce(IV)-substituted... Read More about Probing polyoxometalate-protein interactions using molecular dynamics simulations.

Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes (2016)
Journal Article
Hanson-Heine, M. W. D., Husseini, F. S., Hirst, J. D., & Besley, N. A. (2016). Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes. Journal of Chemical Theory and Computation, 12(4), 1905-1918. https://doi.org/10.1021/acs.jctc.5b01198

Non-linear two-dimensional infrared spectroscopy (2DIR) is most commonly simulated within the framework of the exciton method. The key parameters for these calculations include the frequency of the oscillators within their molecular environments and... Read More about Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes.

Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II (2016)
Journal Article
Mulholland, S., Turpin, E. R., Bonev, B. B., & Hirst, J. (2016). Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II. Scientific Reports, 6(21185), https://doi.org/10.1038/srep21185

Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin/lipid II membrane complexes are currently lac... Read More about Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II.

Molecular simulations and visualization: introduction and overview (2014)
Journal Article
Hirst, J., Glowacki, D., & Baaden, M. (2014). Molecular simulations and visualization: introduction and overview. Faraday Discussions, 169, https://doi.org/10.1039/C4FD90024C

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualizati... Read More about Molecular simulations and visualization: introduction and overview.

New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations (2014)
Journal Article
Turpin, E. R., Mulholland, S., Teale, A. M., Bonev, B. B., & Hirst, J. D. (2014). New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations. RSC Advances, 4(89), 48621-48631. https://doi.org/10.1039/c4ra09897h

Lantibiotics are an important class of naturally occurring antimicrobial peptides containing unusual dehydrated amino acid residues. In order to enable molecular dynamics simulations of lantibiotics, we have developed empirical force field parameters... Read More about New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations.

Accelerating electrostatic pair methods on graphical processing units to study molecules in supercritical carbon dioxide (2014)
Journal Article
Baker, J., & Hirst, J. (2014). Accelerating electrostatic pair methods on graphical processing units to study molecules in supercritical carbon dioxide. Faraday Discussions, 169, https://doi.org/10.1039/C4FD00012A

Traditionally, electrostatic interactions are modelled using Ewald techniques, which provide a good approximation, but are poorly suited to GPU architectures. We use the GPU versions of the LAMMPS MD package to implement and assess the Wolf summation... Read More about Accelerating electrostatic pair methods on graphical processing units to study molecules in supercritical carbon dioxide.

A theoretical study of the activity in Rh-catalyzed hydroformylation: the origin of the enhanced activity of the ?-acceptor phosphinine ligand (2014)
Journal Article
Aguado-Ullate, S., Baker, J., González-González, V., Müller, C., Hirst, J., & Carbó, J. J. (2014). A theoretical study of the activity in Rh-catalyzed hydroformylation: the origin of the enhanced activity of the π-acceptor phosphinine ligand. Catalysis Science and Technology, 4, https://doi.org/10.1039/C3CY00956D

The factors governing the activity in Rh-catalyzed hydroformylation were investigated using a set of computational tools. We performed DFT calculations on the phosphinine- modified Rh catalyst [HRh(CO)3(PC5H2R3)] and compared it to the phosphane-modi... Read More about A theoretical study of the activity in Rh-catalyzed hydroformylation: the origin of the enhanced activity of the ?-acceptor phosphinine ligand.

Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain (2011)
Journal Article
Hussain, A., Shaw, P., & Hirst, J. (2011). Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain. Journal of Cheminformatics, 3(49), https://doi.org/10.1186/1758-2946-3-49

Background: The Elk-1 transcription factor is a member of a group of proteins called ternary complex factors, which serve as a paradigm for gene regulation in response to extracellular signals. Its deregulation has been linked to multiple human dise... Read More about Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain.

Molecular dynamics simulations using graphics processing units (2011)
Journal Article
Baker, J., & Hirst, J. (2011). Molecular dynamics simulations using graphics processing units. Molecular Informatics, 30(6-7), https://doi.org/10.1002/minf.201100042

It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In t... Read More about Molecular dynamics simulations using graphics processing units.

First principles predictions of thermophysical properties of refrigerant mixtures (2011)
Journal Article
Oakley, M. T., Hainam, D., Hirst, J., & Wheatley, R. J. (2011). First principles predictions of thermophysical properties of refrigerant mixtures. Journal of Chemical Physics, 134, https://doi.org/10.1063/1.3567308

We present pair potentials for fluorinated methanes and their dimers with CO2 based on ab initio potential energy surfaces. These potentials reproduce the experimental second virial coefficients of the pure fluorinated methanes and their mixtures wit... Read More about First principles predictions of thermophysical properties of refrigerant mixtures.

Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures (2010)
Journal Article
Kountouris, P., & Hirst, J. D. (2010). Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures. BMC Bioinformatics, 11, Article 407. https://doi.org/10.1186/1471-2105-11-407

Background β-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains. Results We have developed a novel method... Read More about Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures.

Predicting ?-turns and their types using predicted backbone dihedral angles and secondary structures (2010)
Journal Article
Kountouris, P., & Hirst, J. (2010). Predicting ?-turns and their types using predicted backbone dihedral angles and secondary structures. BMC Bioinformatics, 11,

Background: β-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains. Results: We have developed a novel method tha... Read More about Predicting ?-turns and their types using predicted backbone dihedral angles and secondary structures.

Exploring protein structural dissimilarity to facilitate structure classification (2009)
Journal Article
Jain, P., & Hirst, J. (2009). Exploring protein structural dissimilarity to facilitate structure classification. BMC Structural Biology, 9, https://doi.org/10.1186/1472-6807-9-60

Background: Classification of newly resolved protein structures is important in understanding their architectural, evolutionary and functional relatedness to known protein structures. Among various efforts to improve the database of Structural Classi... Read More about Exploring protein structural dissimilarity to facilitate structure classification.