Research Repository

See what's under the surface


Atomistic details of chymotrypsin conformational changes upon adsorption on silica (2018)
Journal Article
Hildebrand, N., Michaelis, M., Wurzler, N., Li, Z., Hirst, J. D., Micsonai, A., …Ciacchi, L. C. (2018). Atomistic details of chymotrypsin conformational changes upon adsorption on silica. ACS Biomaterials Science and Engineering, doi:10.1021/acsbiomaterials.8b00819

Adsorption of enzymes on solid surfaces may lead to conformational changes that reduce their catalytic conversion activity and are thus detrimental to the efficiency of biotechnology or biosensing applications. This work is a joint theoretical and expe... Read More

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, doi:10.1002/minf.201700130. ISSN 1868-1743

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

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, doi:10.1016/j.jmb.2017.12.009. ISSN 0022-2836

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

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, doi:10.1039/C7SC03336B. ISSN 2041-6520

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

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. (in press). Quantum chemical calculations of tryptophan→heme electron and excitation energy transfer rates in myoglobin. Journal of Computational Chemistry, doi:10.1002/jcc.24793. ISSN 0192-8651

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

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, doi:10.1039/C7SC00586E. ISSN 2046-2069

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

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), doi:10.1002/jcc.24674. ISSN 0192-8651

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

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), doi:10.1002/chem.201602263. ISSN 0947-6539

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

Simulation of the two-dimensional infrared spectroscopy of peptides using localized normal modes (2016)
Journal Article
Hanson-Heine, M. W., Husseini, F. S., Hirst, J., & Besley, N. A. (2016). Simulation of the two-dimensional infrared spectroscopy of peptides using localized normal modes. Journal of Chemical Theory and Computation, 12(4), doi:10.1021/acs.jctc.5b01198. ISSN 1549-9618

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

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), doi:10.1038/srep21185. ISSN 2045-2322

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

Vibronic structure in the far-UV electronic circular dichroism spectra of proteins (2015)
Journal Article
Li, Z., Robinson, D., & Hirst, J. (2015). Vibronic structure in the far-UV electronic circular dichroism spectra of proteins. Faraday Discussions, 177, 329-344. doi:10.1039/c4fd00163j

The Franck–Condon effect is considered and the vibrational structure of the πnbπ* transition of the peptide backbone is incorporated into matrix method calculations of the electronic circular dichroism (CD) spectra of proteins in the far-ultraviolet.... Read More

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, doi:10.1039/C4FD90024C. ISSN 1359-6640

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

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, doi:10.1039/C4FD00012A. ISSN 1359-6640

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

A theoretical study of the activity in Rh-catalyzed hydroformylation: the origin of the enhanced activity of the π-acceptor phosphinine ligand (2014)
Journal Article
activity of the π-acceptor phosphinine ligand. Catalysis Science and Technology, 4, doi:10.1039/C3CY00956D. ISSN 2044-4753

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

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), doi:10.1186/1758-2946-3-49. ISSN 1758-2946

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

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), doi:10.1002/minf.201100042. ISSN 1868-1743

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

Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures (2010)
Journal Article
Kountouris, P., & Hirst, J. (2010). Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures. BMC Bioinformatics, 11, ISSN 1471-2105

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

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, doi:10.1186/1472-6807-9-60. ISSN 1472-6807

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