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Artificial intelligence for small molecule anticancer drug discovery (2024)
Journal Article
Duo, L., Liu, Y., Ren, J., Tang, B., & Hirst, J. D. (2024). Artificial intelligence for small molecule anticancer drug discovery. Expert Opinion on Drug Discovery, https://doi.org/10.1080/17460441.2024.2367014

Introduction: The transition from conventional cytotoxic chemotherapy to targeted cancer therapy with small-molecule anticancer drugs has enhanced treatment outcomes. This approach, which now dominates cancer treatment, has several advantages. Despit... Read More about Artificial intelligence for small molecule anticancer drug discovery.

Solvent flashcards: a visualisation tool for sustainable chemistry. (2024)
Journal Article
Heeley, J., Boobier, S., & Hirst, J. D. (2024). Solvent flashcards: a visualisation tool for sustainable chemistry. Journal of Cheminformatics, 16(1), Article 60. https://doi.org/10.1186/s13321-024-00854-9

Selecting greener solvents during experiment design is imperative for greener chemistry. While many solvent selection guides are currently used in the pharmaceutical industry, these are often paper-based guides which can make it difficult to identify... Read More about Solvent flashcards: a visualisation tool for sustainable chemistry..

Discovery of novel SOS1 inhibitors using machine learning (2024)
Journal Article
Duo, L., Chen, Y., Liu, Q., Ma, Z., Farjudian, A., Yong Ho, W., …Tang, B. (2024). Discovery of novel SOS1 inhibitors using machine learning. RSC Medicinal Chemistry, 15(4), 1392-1403. https://doi.org/10.1039/D4MD00063C

Overactivation of the rat sarcoma virus (RAS) signaling is responsible for 30% of all human malignancies. Son of sevenless 1 (SOS1), a crucial node in the RAS signaling pathway, could modulate RAS activation, offering a promising therapeutic strategy... Read More about Discovery of novel SOS1 inhibitors using machine learning.

Applications of Quantum Chemistry in Biomimetic Syntheses of Polycyclic Furanocembrane Derivatives (2024)
Journal Article
Wang, D., Zhou, T., Ren, J., Hirst, J., Gao, Z., & Tang, B. (2024). Applications of Quantum Chemistry in Biomimetic Syntheses of Polycyclic Furanocembrane Derivatives. SYNLETT, https://doi.org/10.1055/a-2239-6577

This paper summarizes the guidance provided by quantum chemical calculations to the biomimetic syntheses of polycyclic marine furanocembrane derivatives. Polycyclic furanocembrane derivatives are a group of structurally complex and biologically impor... Read More about Applications of Quantum Chemistry in Biomimetic Syntheses of Polycyclic Furanocembrane Derivatives.

Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations (2023)
Journal Article
King, T. E., Humphrey, J. R., Laughton, C. A., Thomas, N. R., & Hirst, J. D. (2024). Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations. Journal of Chemical Information and Modeling, 64(1), 265–275. https://doi.org/10.1021/acs.jcim.3c01898

Excipients are included within protein biotherapeutic solution formulations to improve colloidal and conformational stability but are generally not designed for the specific purpose of preventing aggregation and improving cryoprotection in solution.... Read More about Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations.

Electrocatalytic CO2 reduction to C2H4: From lab to fab (2023)
Journal Article
Guo, Z., Yang, F., Li, X., Zhu, H., Do, H., Loon Fow, K., …Xu, M. (2024). Electrocatalytic CO2 reduction to C2H4: From lab to fab. Journal of Energy Chemistry, 90, 540-564. https://doi.org/10.1016/j.jechem.2023.11.019

The global concerns of energy crisis and climate change, primarily caused by carbon dioxide (CO2), are of utmost importance. Recently, the electrocatalytic CO2 reduction reaction (CO2RR) to high value-added multi-carbon (C2+) products driven by renew... Read More about Electrocatalytic CO2 reduction to C2H4: From lab to fab.

Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets (2023)
Journal Article
Douaki, A., Stuber, A., Hengsteler, J., Momotenko, D., Rogers, D. M., Rocchia, W., …Garoli, D. (2023). Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets. Chemical Communications, 59(99), 14713-14716. https://doi.org/10.1039/d3cc04334g

Aptamer-based sensing of small molecules such as dopamine and serotonin in the brain, requires characterization of the specific aptamer sequences in solutions mimicking the in vivo environment with physiological ionic concentrations. In particular, d... Read More about Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets.

Synergistic engineering of heteronuclear Ni-Ag dual-atom catalysts for high-efficiency CO2 electroreduction with nearly 100% CO selectivity (2023)
Journal Article
Guo, Z., Zhu, H., Yang, G., Wu, A., Chen, Q., Yan, Z., …Xu, M. (2023). Synergistic engineering of heteronuclear Ni-Ag dual-atom catalysts for high-efficiency CO2 electroreduction with nearly 100% CO selectivity. Chemical Engineering Journal, 476, Article 146556. https://doi.org/10.1016/j.cej.2023.146556

Single-atom catalysts (SACs) have emerged as attractive materials for the electrocatalytic carbon dioxide reduction (ECO2R). Dual-atom catalysts (DACs), an extension of SACs, exhibit more compelling functionalities due to the synergistic effects betw... Read More about Synergistic engineering of heteronuclear Ni-Ag dual-atom catalysts for high-efficiency CO2 electroreduction with nearly 100% CO selectivity.

ML meets MLn: machine learning in ligand promoted homogeneous catalysis (2023)
Journal Article
Hirst, J. D., Boobier, S., Coughlan, J., Streets, J., Jacob, P. L., Pugh, O., …Woodward, S. (2023). ML meets MLn: machine learning in ligand promoted homogeneous catalysis. Artificial Intelligence Chemistry, 1(2), Article 100006. https://doi.org/10.1016/j.aichem.2023.100006

The benefits of using machine learning approaches in the design, optimisation and understanding of homogeneous catalytic processes are being increasingly realised. We focus on the understanding and implementation of key concepts, which serve as condu... Read More about ML meets MLn: machine learning in ligand promoted homogeneous catalysis.

Predicting bioactivity of antibiotic metabolites by molecular docking and dynamics (2023)
Journal Article
Chio, H., Guest, E. E., Hobman, J. L., Dottorini, T., Hirst, J. D., & Stekel, D. J. (2023). Predicting bioactivity of antibiotic metabolites by molecular docking and dynamics. Journal of Molecular Graphics and Modelling, 123, Article 108508. https://doi.org/10.1016/j.jmgm.2023.108508

Antibiotics enter the environment through waste streams, where they can exert selective pressure for antimicrobial resistance in bacteria. However, many antibiotics are excreted as partly metabolized forms, or can be subject to partial breakdown in w... Read More about Predicting bioactivity of antibiotic metabolites by molecular docking and dynamics.

Dynamic Disorder Drives Exciton Dynamics in Diketopyrrolopyrrole-Thiophene-Containing Molecular Crystals (2023)
Journal Article
Jiang, L., Hirst, J. D., & Do, H. (2023). Dynamic Disorder Drives Exciton Dynamics in Diketopyrrolopyrrole-Thiophene-Containing Molecular Crystals. Journal of Physical Chemistry C, 127(11), 5519-5532. https://doi.org/10.1021/acs.jpcc.2c07984

There is a growing interest in controllable molecular materials for potential nanophotonic and quantum information applications where excitons move beyond the incoherent transport regime. Thus, the ability to identify the key parameters that correlat... Read More about Dynamic Disorder Drives Exciton Dynamics in Diketopyrrolopyrrole-Thiophene-Containing Molecular Crystals.

Krein support vector machine classification of antimicrobial peptides (2023)
Journal Article
Redshaw, J., Ting, D. S., Brown, A., Hirst, J. D., & Gärtner, T. (2023). Krein support vector machine classification of antimicrobial peptides. Digital Discovery, 2(2), 502-511. https://doi.org/10.1039/d3dd00004d

Antimicrobial peptides (AMPs) represent a potential solution to the growing problem of antimicrobial resistance, yet their identification through wet-lab experiments is a costly and time-consuming process. Accurate computational predictions would all... Read More about Krein support vector machine classification of antimicrobial peptides.

Electronic circular dichroism of proteins computed using a diabatisation scheme (2022)
Journal Article
Rogers, D. M., Do, H., & Hirst, J. D. (2023). Electronic circular dichroism of proteins computed using a diabatisation scheme. Molecular Physics, 121(7-8), Article e2133748. https://doi.org/10.1080/00268976.2022.2133748

Circular dichroism (CD) spectroscopy is a powerful technique employed to study the structure of biomolecules. More accurate calculation of CD from first principles will aid both computational and experimental studies of protein structure and dynamics... Read More about Electronic circular dichroism of proteins computed using a diabatisation scheme.

Machine learning for yield prediction for chemical reactions using in situ sensors (2022)
Journal Article
Davies, J. C., Pattison, D., & Hirst, J. D. (2023). Machine learning for yield prediction for chemical reactions using in situ sensors. Journal of Molecular Graphics and Modelling, 118, Article 108356. https://doi.org/10.1016/j.jmgm.2022.108356

Machine learning models were developed to predict product formation from time-series reaction data for ten Buchwald-Hartwig coupling reactions. The data was provided by DeepMatter and was collected in their DigitalGlassware cloud platform. The reacti... Read More about Machine learning for yield prediction for chemical reactions using in situ sensors.

Free energy perturbation calculations of tetrahydroquinolines complexed to the first bromodomain of BRD4 (2022)
Journal Article
Silva, A. F., Guest, E. E., Falcone, B. N., Pickett, S. D., Rogers, D. M., & Hirst, J. D. (2023). Free energy perturbation calculations of tetrahydroquinolines complexed to the first bromodomain of BRD4. Molecular Physics, 121(9-10), Article e2124201. https://doi.org/10.1080/00268976.2022.2124201

Alchemical free energy perturbation (FEP) theory is widely used nowadays to calculate protein–ligand binding energies, often in support of drug discovery endeavours. We assess the accuracy and sensitivity of absolute FEP binding energies with respect... Read More about Free energy perturbation calculations of tetrahydroquinolines complexed to the first bromodomain of BRD4.

N-Hydroxyethyl acrylamide as a functional eROP initiator for the preparation of nanoparticles under “greener” reaction conditions (2022)
Journal Article
Lentz, J. C., Cavanagh, R., Moloney, C., Falcone Pin, B., Kortsen, K., Fowler, H. R., …Howdle, S. M. (2022). N-Hydroxyethyl acrylamide as a functional eROP initiator for the preparation of nanoparticles under “greener” reaction conditions. Polymer Chemistry, 13(42), 6032-6045. https://doi.org/10.1039/d2py00849a

N-Hydroxyethyl acrylamide was used as a functional initiator for the enzymatic ring-opening polymerisation of ϵ-caprolactone and δ-valerolactone. N-Hydroxyethyl acrylamide was found not to undergo self-reaction in the presence of Lipase B from Candid... Read More about N-Hydroxyethyl acrylamide as a functional eROP initiator for the preparation of nanoparticles under “greener” reaction conditions.

Structure–Property Relationships in Amorphous Thieno[3,2-b]thiophene–Diketopyrrolopyrrole–Thiophene-Containing Polymers (2022)
Journal Article
Jiang, L., Hirst, J. D., & Do, H. (2022). Structure–Property Relationships in Amorphous Thieno[3,2-b]thiophene–Diketopyrrolopyrrole–Thiophene-Containing Polymers. Journal of Physical Chemistry C, 126(26), 10842-10854. https://doi.org/10.1021/acs.jpcc.2c01650

(Figure Presented) We present calculations of electronic structure properties of disordered conducting polymers containing thieno[3,2b]thiophene, diketopyrrolopyrrole, and thiophene. Atomistic force field parameters for the polymer were optimized to... Read More about Structure–Property Relationships in Amorphous Thieno[3,2-b]thiophene–Diketopyrrolopyrrole–Thiophene-Containing Polymers.

Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4 (2022)
Journal Article
Guest, E. E., Cervantes, L. F., Pickett, S. D., Brooks, C. L., & Hirst, J. D. (2022). Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. Journal of Chemical Information and Modeling, 62(6), 1458-1470. https://doi.org/10.1021/acs.jcim.1c01229

Accurate and rapid predictions of the binding affinity of a compound to a target are one of the ultimate goals of computer aided drug design. Alchemical approaches to free energy estimations follow the path from an initial state of the system to the... Read More about Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4.

Effect of Oriented Electric Fields on Biologically Relevant Iron–Sulfur Clusters: Tuning Redox Reactivity for Catalysis (2022)
Journal Article
Gaughan, S. J. H., Hirst, J. D., Croft, A. K., & Jäger, C. M. (2022). Effect of Oriented Electric Fields on Biologically Relevant Iron–Sulfur Clusters: Tuning Redox Reactivity for Catalysis. Journal of Chemical Information and Modeling, 62(3), 591-601. https://doi.org/10.1021/acs.jcim.1c00791

Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases, and radical S-Adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyo... Read More about Effect of Oriented Electric Fields on Biologically Relevant Iron–Sulfur Clusters: Tuning Redox Reactivity for Catalysis.

Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1 (2021)
Journal Article
Zhou, J., Wu, S., Lee, B. G., Chen, T., He, Z., Lei, Y., …Hirst, J. D. (2021). Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1. Molecules, 26(24), Article 7492. https://doi.org/10.3390/molecules26247492

A machine learning approach has been applied to virtual screening for lysine specific demethylase 1 (LSD1) inhibitors. LSD1 is an important anti-cancer target. Machine learning models to predict activity were constructed using Morgan molecular finger... Read More about Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1.

Kernel Methods for Predicting Yields of Chemical Reactions (2021)
Journal Article
Haywood, A. L., Redshaw, J., Hanson-Heine, M. W., Taylor, A., Brown, A., Mason, A. M., …Hirst, J. D. (2022). Kernel Methods for Predicting Yields of Chemical Reactions. Journal of Chemical Information and Modeling, 62(9), 2077-2092. https://doi.org/10.1021/acs.jcim.1c00699

The use of machine learning methods for the prediction of reaction yield is an emerging area. We demonstrate the applicability of support vector regression (SVR) for predicting reaction yields, using combinatorial data. Molecular descriptors used in... Read More about Kernel Methods for Predicting Yields of Chemical Reactions.

Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S1 ← S0 Transitions (2021)
Journal Article
Robinson, D., Alarfaji, S. S., & Hirst, J. D. (2021). Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S1 ← S0 Transitions. Journal of Physical Chemistry A, 125(24), 5237–5245. https://doi.org/10.1021/acs.jpca.1c01685

For benzene, toluene, aniline, fluorobenzene, and phenol, even sophisticated treatments of electron correlation, such as MRCI and XMS-CASPT2 calculations, show oscillator strengths typically lower than experiment. Inclusion of a simple pseudo-diabati... Read More about Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S1 ← S0 Transitions.

Structural variation of protein-ligand complexes of the first bromodomain of BRD4 (2021)
Journal Article
Guest, E. E., Pickett, S. D., & Hirst, J. D. (2021). Structural variation of protein-ligand complexes of the first bromodomain of BRD4. Organic and Biomolecular Chemistry, 19(25), 5632-5641. https://doi.org/10.1039/d1ob00658d

The bromodomain-containing protein 4 (BRD4), a member of the bromodomain and extra-terminal domain (BET) family, plays a key role in several diseases, especially cancers. With increased interest in BRD4 as a therapeutic target, many X-ray crystal str... Read More about Structural variation of protein-ligand complexes of the first bromodomain of BRD4.

Near-ultraviolet circular dichroism and two-dimensional spectroscopy of polypeptides (2021)
Journal Article
Segatta, F., Rogers, D. M., Dyer, N. T., Guest, E. E., Li, Z., Do, H., …Hirst, J. D. (2021). Near-ultraviolet circular dichroism and two-dimensional spectroscopy of polypeptides. Molecules, 26(2), Article 396. https://doi.org/10.3390/MOLECULES26020396

A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ul... Read More about Near-ultraviolet circular dichroism and two-dimensional spectroscopy of polypeptides.

A Machine Learning Protocol for Predicting Protein Infrared Spectra (2020)
Journal Article
Ye, S., Zhong, K., Zhang, J., Hu, W., Hirst, J. D., Zhang, G., …Jiang, J. (2020). A Machine Learning Protocol for Predicting Protein Infrared Spectra. Journal of the American Chemical Society, 142(45), 19071–19077. https://doi.org/10.1021/jacs.0c06530

© 2020 American Chemical Society. Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive... Read More about A Machine Learning Protocol for Predicting Protein Infrared Spectra.

Computed optical spectra of SARS-CoV-2 proteins (2020)
Journal Article
Li, Z., & Hirst, J. D. (2020). Computed optical spectra of SARS-CoV-2 proteins. Chemical Physics Letters, 758, Article 137935. https://doi.org/10.1016/j.cplett.2020.137935

© 2020 Elsevier B.V. Treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes Covid-19, may well be predicated on knowledge of the structures of protein of this virus. However, often these cannot be determined... Read More about Computed optical spectra of SARS-CoV-2 proteins.

Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid (2020)
Journal Article
Spankie, T. J., Haywood, A. L., Dottorini, T., Barrow, P. A., & Hirst, J. D. (2020). Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid. Journal of Molecular Graphics and Modelling, 101, Article 107723. https://doi.org/10.1016/j.jmgm.2020.107723

© 2020 Elsevier Inc. One promising strategy to combat antimicrobial resistance is to use bacteriophages that attach to the sex pili produced by transmissible antimicrobial resistance (AMR) plasmids, infect AMR bacteria and select for loss of the AMR... Read More about Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction (2020)
Journal Article
Baiz, C. R., Błasiak, B., Bredenbeck, J., Cho, M., Choi, J. H., Corcelli, S. A., …Zanni, M. T. (2020). Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chemical Reviews, 120(15), 7152–7218. https://doi.org/10.1021/acs.chemrev.9b00813

© 2020 American Chemical Society. Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have b... Read More about Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Unfolding Dynamics of a Photoswitchable Helical Peptide (2020)
Journal Article
Auvray, F., & Hirst, J. D. (2020). Unfolding Dynamics of a Photoswitchable Helical Peptide. Journal of Physical Chemistry B, 124(26), 5380-5392. https://doi.org/10.1021/acs.jpcb.0c04017

We present an atomistic force field for the azo-moiety of the photoswitchable FK-11-X peptide. We use the parameters to study the unfolding of the peptide through molecular dynamics simulations. The unfolded ensemble contains many different structure... Read More about Unfolding Dynamics of a Photoswitchable Helical Peptide.

Molecular Simulation of αvβ6 Integrin Inhibitors (2020)
Journal Article
Guest, E. E., Oatley, S. A., Macdonald, S. J. F., & Hirst, J. D. (2020). Molecular Simulation of αvβ6 Integrin Inhibitors. Journal of Chemical Information and Modeling, 60(11), 5487-5498. https://doi.org/10.1021/acs.jcim.0c00254

The urgent need for new treatments for the chronic lung disease idiopathic pulmonary fibrosis (IPF) motivates research into antagonists of the RGD binding integrin αvβ6, a protein linked to the initiation and progression of the disease. Molecular dyn... Read More about Molecular Simulation of αvβ6 Integrin Inhibitors.

Late-Stage Functionalization by Chan–Lam Amination: Rapid Access to Potent and Selective Integrin Inhibitors (2020)
Journal Article
Robinson, H., Oatley, S., Rowedder, J., Slade, P., Macdonald, S., Argent, S., …Moody, C. J. (2020). Late-Stage Functionalization by Chan–Lam Amination: Rapid Access to Potent and Selective Integrin Inhibitors. Chemistry - A European Journal, 26(34), 7678-7684. https://doi.org/10.1002/chem.202001059

© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim A late-stage functionalization of the aromatic ring in amino acid derivatives is described. The key step is a copper-catalysed diversification of a boronate ester by amination (Chan–Lam reaction) th... Read More about Late-Stage Functionalization by Chan–Lam Amination: Rapid Access to Potent and Selective Integrin Inhibitors.

Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization (2019)
Journal Article
Auvray, F., Dennetiere, D., Giuliani, A., Jamme, F., Wien, F., Nay, B., …Réfrégiers, M. (2019). Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization. Structural Dynamics, 6(5), Article 054307. https://doi.org/10.1063/1.5120346

Ultraviolet (UV) synchrotron radiation circular dichroism (SRCD) spectroscopy has made an important contribution to the determination and understanding of the structure of bio-molecules. In this paper, we report an innovative approach that we term ti... Read More about Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization.

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.

Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra (2019)
Journal Article
Michaelis, M., Hildebrand, N., Meißner, R. H., Wurzler, N., Li, Z., Hirst, J. D., …Colombi Ciacchi, L. (2019). Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra. Journal of Physical Chemistry B, 123(31), 6694-6704. https://doi.org/10.1021/acs.jpcb.9b03932

Although successful in the structural determination of ordered biomolecules, the spectroscopic investigation of oligopeptides in solution is hindered by their complex and rapidly changing conformational ensemble. The measured circular dichroism (CD)... Read More about Impact of the Conformational Variability of Oligopeptides on the Computational Prediction of Their CD Spectra.

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, 4(12), 4036-4050. https://doi.org/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 about Atomistic details of chymotrypsin conformational changes upon adsorption on silica.

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.

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.

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 π-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 π-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 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,

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 β-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.