1993 …2023

Research output per year

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Research Output

2020

Cyclic boronates as versatile scaffolds for KPC-2 β-lactamase inhibition

Tooke, C. L., Hinchliffe, P., Kranjnc, A., Mulholland, A. J., Brem, J., Schofield, C. J. & Spencer, J., 10 Jan 2020, In : Medicinal Chemistry. 6 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
40 Downloads (Pure)

Discovery of New and Potent InhA Inhibitors as Anti-tuberculosis Agents: Structure Based Virtual Screening Validated by Biological Assays and X-ray Crystallography

Kamsri, P., Hanwarinroj, C., Phusi, N., Pornprom, T., Chayajarus, K., Punkvang, A., Suttipanta, N., Srimanote, P., Suttisintong, K., Songsiriritthigul, C., Saparpakorn, P., Hannongbua, S., Rattanabunyong, S., Seetaha, S., Choowongkomon, K., Sureram, S., Kittakoop, P., Hongmanee, P., Santanirand, P., Chen, Z. & 7 others, Zhu, W., Blood, R. A., Takebayashi, Y., Hinchliffe, P., Mulholland, A. J., Spencer, J. & Pungpo, P., 27 Jan 2020, In : Journal of Chemical Information and Modeling. 60 (2020), 1, p. 226-234 9 p.

Research output: Contribution to journalArticle (Academic Journal)

Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking

Deeks, H. M., Walters, R. K., Hare, S. R., O’Connor, M. B., Mulholland, A. J. & Glowacki, D. R., 11 Mar 2020, In : PLoS ONE. 15, 3, 21 p., e0228461.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
18 Downloads (Pure)

Visualizing the protons in a metalloenzyme electron proton transfer pathway

Kwon, H., Basran, J., Devos, J. M., Suardiaz Del Rio, R., Van Der Kamp, M. W., Mulholland, A. J., Schrader, T. E., Ostermann, A., Blakeley, M. P., Moody, P. C. E. & Raven, E., 9 Mar 2020, In : Proceedings of the National Academy of Sciences of the United States of America.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
103 Downloads (Pure)
2019

A General Mechanism for Signal Propagation in the Nicotinic Acetylcholine Receptor Family

Oliveira, A. S. F., Edsall, C. J., Woods, C. J., Bates, P., Nunez, G. V., Wonnacott, S., Bermudez, I., Ciccotti, G., Gallagher, T., Sessions, R. B. & Mulholland, A. J., 26 Dec 2019, In : Journal of the American Chemical Society. 141, 51, p. 19953-19958 6 p., 51.

Research output: Contribution to journalArticle (Academic Journal)

An Efficient Computational Assay for β-Lactam Antibiotic Breakdown by Class A β-Lactamases

Hirvonen, V., Hammond, K., Chudyk, E., Limb, M., Spencer, J., Mulholland, A. & Van der Kamp, M., 30 Jul 2019, In : Journal of Chemical Information and Modeling. 59, 8, p. 3365-3369 5 p.

Research output: Contribution to journalArticle (Academic Journal)

A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Unfolding of G-Quadruplex DNA

O'Hagan, M., Haldar, S., Duchi, M., Oliver, T. A. A., Mulholland, A., Morales, J. C. & Galan, C., 22 Mar 2019, In : Angewandte Chemie - International Edition. 58, 13, p. 4334-4338 5 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
7 Citations (Scopus)
30 Downloads (Pure)

BioSimSpace: An interoperable Python framework for biomolecular simulation

Hedges, L. O., Mey, A. S. J. S., Laughton, C., Gervasio, F. L., Mulholland, A. J., Woods, C. J. & Michel, J., 22 Nov 2019, In : Journal of Open Source Software. 4, 1831.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
15 Downloads (Pure)

Emergence of a Negative Activation Heat Capacity during Evolution of a Designed Enzyme

Bunzel, A., Kries, H., Marchetti, L., Zeymer, C., Mittl, P. R. E., Mulholland, A. & Hilvert, D., 31 Jul 2019, In : Journal of the American Chemical Society. 141, 30, p. 11745-11748 4 p.

Research output: Contribution to journalArticle (Academic Journal)

Identification of the Initial Steps in Signal Transduction in the α4β2 Nicotinic Receptor: Insights from Equilibrium and Nonequilibrium Simulations

Oliveira, A. S. F., Shoemark, D. K., Campello, H. R., Wonnacott, S., Gallagher, T., Sessions, R. B. & Mulholland, A. J., 2 Jul 2019, In : Structure. 27, 7, p. 1171-1183.e3 17 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
1 Citation (Scopus)
6 Downloads (Pure)

IMPRESSION – prediction of NMR parameters for 3-dimensional chemical structures using machine learning with near quantum chemical accuracy

Gerrard, W., Bratholm, L. A., Packer, M. J., Mulholland, A. J., Glowacki, D. R. & Butts, C. P., 18 Nov 2019, (Accepted/In press) In : Chemical Science. 11, 2, p. 508-515 8 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
1 Citation (Scopus)
43 Downloads (Pure)

In silico study directed towards identification of the key structural features of GyrB inhibitors targeting MTB DNA gyrase: HQSAR, CoMSIA and molecular dynamics simulations

Kamsri, P., Punkvang, A., Hannongbua, S., Suttisintong, K., Kittakoop, P., Spencer, J., Mulholland, A. J. & Pungpo, P., 2 Nov 2019, In : SAR and QSAR in Environmental Research. 30, 11, p. 775-800 27 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
4 Citations (Scopus)
157 Downloads (Pure)

Limitations of ligand-only approaches for predicting the reactivity of covalent inhibitors

Voice, A., Tresadern, G., van Vlijmen, H. & Mulholland, A. J., 24 Sep 2019, In : Journal of Chemical Information and Modeling. 8 p.

Research output: Contribution to journalArticle (Academic Journal)

Molecular dynamics simulation framework to probe the binding hypothesis of CYP3A4 inhibitors

Kiani, Y. S., Ranaghan, K. E., Jabeen, I. & Mulholland, A. J., 10 Sep 2019, In : International Journal of Molecular Sciences. 20, 18, 23 p., 4468.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
2 Citations (Scopus)
93 Downloads (Pure)

Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution

Ranaghan, K. E., Shchepnovska, D., Bennie, S. J., Lawan, N., Macrae, S., Zurek, J., Manby, F. R. & Mulholland, A. J., 28 May 2019, In : Journal of Chemical Information and Modeling. 59, 5, p. 2063-2078 16 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
7 Citations (Scopus)
63 Downloads (Pure)

Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate

Nutho, B., Mulholland, A. J. & Rungrotmongkol, T., 4 Apr 2019, In : Journal of Physical Chemistry B. 123, 13, p. 2889-2903 15 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
3 Citations (Scopus)
38 Downloads (Pure)

Quantum Mechanics/Molecular Mechanics Simulations Show Saccharide Distortion is Required for Reaction in Hen Egg-White Lysozyme

Limb, M. A. L., Suardiaz Del Rio, R., Grant, I. M. & Mulholland, A., 15 Jan 2019, In : Chemistry - A European Journal. 25, 3, p. 764-768 5 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
44 Downloads (Pure)

Simulations of Shikimate Dehydrogenase from Mycobacterium tuberculosis in Complex with 3-Dehydroshikimate and NADPH Suggest Strategies for MtbSDH Inhibition

Punkvang, A., Kamsri, P., Mulholland, A., Spencer, J., Hannongbua, S. & Pungpo, P., 22 Apr 2019, In : Journal of Chemical Information and Modeling. 59, 4, p. 1422-1433 12 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
28 Downloads (Pure)

Taming the reactivity of monoterpene synthases to guide regioselective product hydroxylation

Leferink, N. G. H., Ranaghan, K. E., Battye, J., Johannissen, L. O., Hay, S., Van Der Kamp, M. W., Mulholland, A. J. & Scrutton, N. S., 3 Dec 2019, In : ChemBioChem. 7 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
143 Downloads (Pure)

Teaching Enzyme Catalysis Using Interactive Molecular Dynamics in Virtual Reality

Bennie, S., Deeks, H., Glowacki, D., O'Connor, M., Mulholland, A. & Ranaghan, K., 31 Jul 2019, In : Journal of Chemical Education.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
125 Downloads (Pure)

Visualizing protein–ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site

Raza, S., Ranaghan, K., Van der Kamp, M., Woods, C., Mulholland, A. & Azam, S. S., 15 May 2019, In : Journal of Computer-Aided Molecular Design. 33, 5, p. 461-475 15 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
2 Citations (Scopus)
34 Downloads (Pure)
2018

A multiscale simulation approach to modelling drug-protein binding kinetics

Haldar, S., Comitani, F., Saladino, G., Woods, C., Van der Kamp, M., Mulholland, A. & Gervasio, F. L., 13 Sep 2018, In : Journal of Chemical Theory and Computation. 9 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
118 Downloads (Pure)

Biocatalytic Routes to Lactone Monomers for Polymer Production

Messiha, H. L., Ahmed, S. T., Karuppiah, V., Suardiaz, R., Ascue Avalos, G. A., Fey, N., Yeates, S., Toogood, H. S., Mulholland, A. J. & Scrutton, N. S., 3 Apr 2018, In : Biochemistry. 57, 13, p. 1997-2008 12 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
19 Citations (Scopus)
335 Downloads (Pure)

Biomolecular simulations: from dynamics and mechanisms to computational assays of biological activity

Huggins, D. J., Biggin, P. C., Dämgen, M. A., Essex, J. W., Harris, S. A., Henchman, R. H., Khalid, S., Kuzmanic, A., Laughton, C. A., Michel, J., Mulholland, A. J., Rosta, E., Sansom, M. S. P. & van der Kamp, M. W., 27 Sep 2018, In : Wiley Interdisciplinary Reviews: Computational Molecular Science. 23 p., e1393.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
22 Citations (Scopus)
165 Downloads (Pure)

Combined Quantum Mechanics and Molecular Mechanics Studies of Enzymatic Reaction Mechanisms

Ainsley, J., Lodola, A., Mulholland, A. J., Christov, C. Z. & Karabencheva-Christova, T. G., 13 Aug 2018, Computational Molecular Modelling in Structural Biology. Karabencheva-Christova, T. G. & Christov, C. Z. (eds.). Elsevier Inc., p. 1-32 32 p. (Advances in Protein Chemistry and Structural Biology; vol. 113).

Research output: Chapter in Book/Report/Conference proceedingChapter in a book

1 Citation (Scopus)

De Novo-Designed α-Helical Barrels as Receptors for Small Molecules

Thomas, F., Dawson, W., Lang, E., Burton, A., Bartlett, G., Rhys, G., Mulholland, A. & Woolfson, D., 20 Jul 2018, In : ACS Synthetic Biology. 7, 7, p. 1808-1816 9 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
14 Citations (Scopus)
157 Downloads (Pure)

Dynamical origins of heat capacity changes in enzyme-catalysed reactions

Van Der Kamp, M. W., Prentice, E. J., Kraakman, K. L., Connolly, M., Mulholland, A. J. & Arcus, V. L., 21 Mar 2018, In : Nature Communications. 9, 1, 7 p., 1177.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
21 Citations (Scopus)
220 Downloads (Pure)

Experiment and Simulation Reveal How Mutations in Functional Plasticity Regions Guide Plant Monoterpene Synthase Product Outcome

Leferink, N. G. H., Ranaghan, K. E., Karuppiah, V., Currin, A., Van Der Kamp, M. W., Mulholland, A. J. & Scrutton, N. S., 4 May 2018, In : ACS Catalysis. 8, 5, p. 3780-3791 12 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
4 Citations (Scopus)
248 Downloads (Pure)

L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib

Callegari, D., Ranaghan, K., Woods, C., Minari, R., Tiseo, M., Mor, M., Mulholland, A. & Lodola, A., 12 Feb 2018, In : Chemical Science. 10 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
254 Downloads (Pure)

Loop Motion in Triosephosphate Isomerase is not a Simple Open and Shut Case

Liao, Q., Kulkarni, Y., Sengupta, U., Petrovic, D., Mulholland, A., Van der Kamp, M., Strodel, B. & Kamerlin, S. C. L., 21 Nov 2018, In : Journal of the American Chemical Society. 140, 46, p. 15889-15903 15 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
12 Citations (Scopus)
336 Downloads (Pure)

Maintaining and breaking symmetry in homomeric coiled-coil assemblies

Rhys, G., Wood, C. W., Lang, E. J. M., Mulholland, A., Brady, R. L., Thomson, A. & Woolfson, D., 8 Oct 2018, In : Nature Communications. 9, 1, 12 p., 4132.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
4 Citations (Scopus)
162 Downloads (Pure)
Open Access
File
213 Downloads (Pure)

Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures

Amaro, R. E. & Mulholland, A. J., 11 Apr 2018, In : Nature reviews. Chemistry. 2, 4, 0148.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
104 Downloads (Pure)

Multiscale simulations of clavulanate inhibition identify the reactive complex in class A β-lactamases and predict efficiency of inhibition

Fritz, R., Alzate-Morales, J. H., Spencer, J., Mulholland, A. J. & Van Der Kamp, M. W., 29 May 2018, In : Biochemistry. 4 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
6 Citations (Scopus)
149 Downloads (Pure)

QM/MM simulations identify the determinants of catalytic activity differences between type ii dehydroquinase enzymes

Lence Quintana, E., Van der Kamp, M., González-Bello, C. & Mulholland, A., 16 May 2018, In : Organic and Biomolecular Chemistry. 16, 24, p. 4443-4455

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
209 Downloads (Pure)

Sampling molecular conformations and dynamics in a multiuser virtual reality framework

O'Connor, M., Deeks, H., Dawn, E., Metatla, O., Roudaut, A., Sutton, M., Thomas, L. M. M., Glowacki, B. R., Sage, R., Tew, P., Wonnacott, M., Bates, P., Mulholland, A. & Glowacki, D., 29 Jun 2018, In : Science Advances. 4, 6, 10 p., eaat2731.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
25 Citations (Scopus)
117 Downloads (Pure)

Sampling molecular conformations and dynamics in a multi-user virtual reality framework

Connor, M. O., Deeks, H. M., Dawn, E., Metatla, O., Roudaut, A., Sutton, M., Glowacki, B. R., Sage, R., Tew, P., Wonnacott, M., Bates, P., Mulholland, A. J. & Glowacki, D. R., 9 Jan 2018, In : arXiv.

Research output: Contribution to journalArticle (Academic Journal)

File
114 Downloads (Pure)

Structural Insights from Molecular Dynamics Simulations of Tryptophan 7-Halogenase and Tryptophan 5-Halogenase

Ainsley, J., Mulholland, A. J., Black, G. W., Sparagano, O., Christov, C. Z. & Karabencheva-Christova, T. G., 31 May 2018, In : ACS Omega. 3, 5, p. 4847-4859 13 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
2 Citations (Scopus)
256 Downloads (Pure)

Understanding Complex Mechanisms of Enzyme Reactivity: The Case of Limonene-1,2-Epoxide Hydrolases

Rinaldi, S., Van Der Kamp, M. W., Ranaghan, K. E., Mulholland, A. J. & Colombo, G., 6 Jul 2018, In : ACS Catalysis. 8, 7, p. 5698-5707 10 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
7 Citations (Scopus)
173 Downloads (Pure)

Unlocking Nicotinic Selectivity via Direct C‒H Functionalization of ()-Cytisine

Rego Campello, H., Garcia Del Villar, S., Honraedt, A., Minguez Viñas, T., Oliveira, S., Ranaghan, K., Shoemark, D., Bermudez, I., Gotti, C., Sessions, R., Mulholland, A., Wonnacott, S. & Gallagher, T., 12 Jul 2018, In : Chem. 4, 7, p. 1710-1725 16 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
6 Citations (Scopus)
178 Downloads (Pure)
2017

Ab Initio QM/MM Modeling of the Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic Amine Dehydrogenase

Ranaghan, K., Mulholland, A., Harvey, J., Manby, F., Scrutton, N., Senthilkumar, K., Morris, W., Johannissen, L. & Masgrau, L., 20 Sep 2017, In : Journal of Physical Chemistry B. 121, 42, p. 9785–9798

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
4 Citations (Scopus)
292 Downloads (Pure)

Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme

Watkins, D. W., Jenkins, J. M. X., Grayson, K. J., Wood, N., Steventon, J. W., Le Vay, K., Goodwin, M. I., Mullen, A. S., Bailey, H. J., Crump, M. P., MacMillan, F., Mulholland, A. J., Cameron, G., Sessions, R. B., Mann, S. & Anderson, J. L. R., 25 Aug 2017, In : Nature Communications. 8, 9 p., 358.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
29 Citations (Scopus)
401 Downloads (Pure)

Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations

Ge, Y., van der Kamp, M., Malaisree, M., Liu, D., Liu, Y. & Mulholland, A. J., 1 Nov 2017, In : Journal of Computer-Aided Molecular Design. 31, 11, p. 995-1007 13 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
7 Citations (Scopus)
236 Downloads (Pure)

Insights into the Mechanistic Basis of Plasmid-Mediated Colistin Resistance from the Crystal Structure of the Catalytic Domain of MCR-1

Hinchliffe, P., Yang, Q., Portal, E., Young, T., Li, H., Tooke, C., Mendes de Carvalho, M., Paterson, N., Brem, J., Ritivirool, P., Tansawai, U., Lei, L., Li, M., Shen, Z., Wang, Y., Schofield, C., Mulholland, A., Shen, J., Walsh, T., Fey, N. & 1 others, Spencer, J., 6 Jan 2017, In : Scientific Reports. 7, 10 p., 39392 .

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
53 Citations (Scopus)
202 Downloads (Pure)

Mechanistic Insights into the Reaction of Chlorination of Tryptophan Catalyzed by Tryptophan 7-Halogenase

Karabencheva-Christova, T. G., Torras, J., Mulholland, A. J., Lodola, A. & Christov, C. Z., 12 Dec 2017, In : Scientific Reports. 7, 15 p., 17395.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
8 Citations (Scopus)
194 Downloads (Pure)

Quantum mechanics/molecular mechanics simulations identify the ring-opening mechanism of creatininase

Jitonnom, J., Mujika, J. I., van der Kamp, M. W. & Mulholland, A. J., 15 Nov 2017, In : Biochemistry. 56, 48, p. 6377-6388 12 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
5 Citations (Scopus)
151 Downloads (Pure)

Rapid estimation of catalytic efficiency by cumulative atomic multipole moments: application to ketosteroid isomerase mutants

Beker, W. L., Van der Kamp, M. W., Mulholland, A. J. & Sokalski, W. A., 14 Feb 2017, In : Journal of Chemical Theory and Computation. 13, 2, p. 945-955 11 p.

Research output: Contribution to journalArticle (Academic Journal)

Open Access
File
4 Citations (Scopus)
212 Downloads (Pure)