CCP-BioSim: Biomolecular simulation at the life sciences interface

2024

Sire: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs

Woods, C. J., Hedges, L. O., Mulholland, A. J., Malaisree, M., Tosco, P., Loeffler, H. H., Suruzhon, M., Burman, M., Bariami, S., Bosisio, S., Calabro, G., Clark, F., Mey, A. S. J. S. & Michel, J., 30 May 2024, In: The Journal of Chemical Physics. 160, 10 p., 202503.

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7 Citations (Scopus)

30 Downloads (Pure)

2018

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

Callegari, D., Ranaghan, K. E., Woods, C. J., Minari, R., Tiseo, M., Mor, M., Mulholland, A. J. & Lodola, A., 14 Mar 2018, In: Chemical Science. 9, 10, p. 2740-2749 10 p.

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76 Citations (Scopus)

345 Downloads (Pure)

Multiscale analysis of enantioselectivity in enzyme-catalysed ‘lethal synthesis’ using projector-based embedding

Zhang, X., Bennie, S., Van der Kamp, M., Glowacki, D., Manby, F. & Mulholland, A., 14 Feb 2018, (E-pub ahead of print) In: Royal Society Open Science. 5, 9 p., 171390.

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21 Citations (Scopus)

303 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 Sept 2017, In: Journal of Physical Chemistry B. 121, 42, p. 9785–9798

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16 Citations (Scopus)

630 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.

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16 Citations (Scopus)

455 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.

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19 Citations (Scopus)

450 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.

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11 Citations (Scopus)

404 Downloads (Pure)

2016

A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase

Bennie, S., Van der Kamp, M., Pennifold, R., Stella, M., Manby, F. & Mulholland, A., 14 Jun 2016, In: Journal of Chemical Theory and Computation. 12, 6, p. 2689-2697 9 p.

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60 Citations (Scopus)

483 Downloads (Pure)

Elucidation of Nonadditive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study

Calabrò, G., Woods, C. J., Powlesland, F., Mey, A. S. J. S., Mulholland, A. J. & Michel, J., 23 Jun 2016, In: Journal of Physical Chemistry B. 120, 24, p. 5340-5350 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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27 Citations (Scopus)

414 Downloads (Pure)

Quantum mechanics/molecular mechanics modeling of drug metabolism: Mexiletine N-hydroxylation by cytochrome P450 1A2

Lonsdale, R., Fort, R., Rydberg, P., Harvey, J. & Mulholland, A., 20 Jun 2016, In: Chemical Research in Toxicology. 29, 6, p. 963-971 9 p.

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29 Citations (Scopus)

490 Downloads (Pure)

The Catalytic Mechanism of a Natural Diels-Alderase Revealed in Molecular Detail

Byrne, M. J., Lees, N. R., Han, L. C., Van Der Kamp, M. W., Mulholland, A. J., Stach, J. E. M., Willis, C. L. & Race, P. R., 18 May 2016, In: Journal of the American Chemical Society. 138, 19, p. 6095-6098 4 p.

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138 Citations (Scopus)

969 Downloads (Pure)

2015

A "Stepping Stone" Approach for Obtaining Quantum Free Energies of Hydration

Sampson, C., Fox, T., Tautermann, C., Woods, C. & Skylaris, C.-K., 11 Jun 2015, In: Journal of Physical Chemistry B. 119, 23, p. 7030-7040

Research output: Contribution to journal › Article (Academic Journal) › peer-review

34 Citations (Scopus)

Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: Free energies of binding of water molecules in influenza neuraminidase

Woods, C. J., Shaw, K. E. & Mulholland, A. J., 22 Jan 2015, In: Journal of Physical Chemistry B. 119, 3, p. 997-1001 5 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

23 Citations (Scopus)

High-level QM/MM calculations support the concerted mechanism for Michael addition and covalent complex formation in thymidylate synthase

Kaiyawet, N., Lonsdale, R., Rungrotmongkol, T., Mulholland, A. J. & Hannongbua, S., 10 Feb 2015, In: Journal of Chemical Theory and Computation. 11, 2, p. 713-722 10 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

21 Citations (Scopus)

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

Gray, A., Harlen, O. G., Harris, S. A., Khalid, S., Leung, Y. M., Lonsdale, R., Mulholland, A. J., Pearson, A. R., Read, D. J. & Richardson, R. A., 1 Jan 2015, In: Acta Crystallographica Section D: Biological Crystallography. D71, 1, p. 162-172 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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9 Citations (Scopus)

313 Downloads (Pure)

2014

A catalytic role for methionine revealed by a combination of computation and experiments on phosphite dehydrogenase

Ranaghan, K. E., Hung, J. E., Bartlett, G. J., Mooibroek, T. J., Harvey, J. N., Woolfson, D. N., van der Donk, W. A. & Mulholland, A. J., 2014, In: Chemical Science. 5, 6, p. 2191-2199 9 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

35 Citations (Scopus)

A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes

Lonsdale, R., Rouse, S. L., Sansom, M. S. P. & Mulholland, A. J., 17 Jul 2014, In: PLoS Computational Biology. 10, 7, e1003714.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

45 Citations (Scopus)

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

Mlýnský, V., Banáš, P., Šponer, J., van der Kamp, M. W., Mulholland, A. J. & Otyepka, M., 13 Feb 2014, In: Journal of Chemical Theory and Computation. 10, 4, p. 1608-1622 15 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

57 Citations (Scopus)

Large-scale density functional theory transition state searching in enzymes

Lever, G., Cole, D. J., Lonsdale, R., Ranaghan, K. E., Wales, D. J., Mulholland, A. J., Skylaris, C. K. & Payne, M. C., 6 Nov 2014, In: Journal of Physical Chemistry Letters. 5, 21, p. 3614-3619 6 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

50 Citations (Scopus)

QM/MM modelling of drug-metabolizing enzymes

Lonsdale, R. & Mulholland, A. J., 2014, In: Current Topics in Medicinal Chemistry. 14, 11, p. 1339-1347 9 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

23 Citations (Scopus)

QM/MM simulations as an assay for carbapenemase activity in class A β-lactamases

Chudyk, E. I., Limb, M. A. L., Jones, C., Spencer, J., van der Kamp, M. W. & Mulholland, A. J., 7 Dec 2014, In: Chemical Communications. 50, 94, p. 14736-14739 4 p.

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41 Citations (Scopus)

350 Downloads (Pure)

QM/MM simulations indicate that Asp185 is the likely catalytic base in the enzymatic reaction of HIV-1 reverse transcriptase

Rungrotmongkol, T., Mulholland, A. J. & Hannongbua, S., May 2014, In: MedChemComm. 5, 5, p. 593-596 4 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

10 Citations (Scopus)

Rapid decomposition and visualisation of protein-ligand binding free energies by residue and by water

Woods, C. J., Malaisree, M., Michel, J., Long, B., McIntosh-Smith, S. & Mulholland, A. J., 1 Jan 2014, In: Faraday Discussions. 169, p. 477-499 23 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

83 Citations (Scopus)

Reaction Mechanism of N-Acetylneuraminic Acid Lyase Revealed by a Combination of Crystallography, QM/MM Simulation, and Mutagenesis

Daniels, A. D., Campeotto, I., van der Kamp, M. W., Bolt, A. H., Trinh, C. H., Phillips, S. E. V., Pearson, A. R., Nelson, A., Mulholland, A. J. & Berry, A., Apr 2014, In: ACS Chemical Biology. 9, 4, p. 1025-1032 8 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

42 Citations (Scopus)

Role of active site residues in promoting cobalt-carbon bond Homolysis in adenosylcobalamin-dependent Mutases revealed through experiment and computation

Roman-Melendez, G. D., von Glehn, P., Harvey, J. N., Mulholland, A. J. & Marsh, E. N. G., 14 Jan 2014, In: Biochemistry. 53, 1, p. 169-177 9 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

23 Citations (Scopus)

Trends in predicted chemoselectivity of cytochrome P450 oxidation: B3LYP barrier heights for epoxidation and hydroxylation reactions

Rydberg, P., Lonsdale, R., Harvey, J. N., Mulholland, A. J. & Olsen, L., Jul 2014, In: Journal of Molecular Graphics and Modelling. 52, p. 30-35 6 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

27 Citations (Scopus)

2013

Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology

van der Kamp, M. W. & Mulholland, A. J., 23 Apr 2013, In: Biochemistry. 52, 16, p. 2708-28 21 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

526 Citations (Scopus)

Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity

Woods, C. J., Malaisree, M., Long, B. J. O., McIntosh-Smith, S. N. & Mulholland, A. J., 20 Dec 2013, In: Scientific Reports. 3, 6 p., 3561.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

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37 Citations (Scopus)

402 Downloads (Pure)

Conformational Change and Ligand Binding in the Aristolochene Synthase Catalytic Cycle

van der Kamp, M. W., Sirirak, J., Zurek, J., Allemann, R. K. & Mulholland, A. J., 12 Nov 2013, In: Biochemistry. 52, 45, p. 8094-8105 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

33 Citations (Scopus)

Conformational Effects on the pro-S Hydrogen Abstraction Reaction in Cyclooxygenase-1: An Integrated QM/MM and MD Study

Christov, C. Z., Lodola, A., Karabencheva-Christova, T. G., Wan, S., Coveney, P. V. & Mulholland, A. J., 5 Mar 2013, In: Biophysical Journal. 104, 5, p. L5-L7 3 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

27 Citations (Scopus)

25 Downloads (Pure)

Nonempirical Energetic Analysis of Reactivity and Covalent Inhibition of Fatty Acid Amide Hydrolase

Chudyk, E. I., Dyguda-Kazimierowicz, E., Langner, K. M., Sokalski, W. A., Lodola, A., Mor, M., Sirirak, J. & Mulholland, A. J., 6 Jun 2013, In: Journal of Physical Chemistry B. 117, 22, p. 6656-6666 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

12 Citations (Scopus)

QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis

van der Kamp, M. W., Chaudret, R. & Mulholland, A. J., Jul 2013, In: FEBS Journal. 280, 13, p. 3120-3131 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

31 Citations (Scopus)

Quantum mechanics/molecular mechanics modeling of fatty acid amide hydrolase reactivation distinguishes substrate from irreversible covalent inhibitors

Lodola, A., Capoferri, L., Rivara, S., Tarzia, G., Piomelli, D., Mulholland, A. & Mor, M., 28 Mar 2013, In: Journal of Medicinal Chemistry. 56, 6, p. 2500-2512 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

36 Citations (Scopus)

Quantum Mechanics/Molecular Mechanics Modeling of Regioselectivity of Drug Metabolism in Cytochrome P450 2C9

Lonsdale, R., Houghton, K. T., Zurek, J., Bathelt, C. M., Foloppe, N., de Groot, M. J., Harvey, J. N. & Mulholland, A. J., 29 May 2013, In: Journal of the American Chemical Society. 135, 21, p. 8001-8015 15 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

134 Citations (Scopus)

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

Luk, L., Dawson, W. M., Roca, M., Moliner, V., Allemann, R., Mulholland, A. J., Harvey, J. N., Glowacki, D. R., Loveridge, J., Javier Ruiz Pernia, J. & Tuñón , I., 8 Oct 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 41, p. 16344–16349

Research output: Contribution to journal › Article (Academic Journal) › peer-review

123 Citations (Scopus)

31 Downloads (Pure)

2012

Determinants of Reactivity and Selectivity in Soluble Epoxide Hydrolase from Quantum Mechanics/Molecular Mechanics Modeling

Lonsdale, R., Hoyle, S., Grey, D. T., Ridder, L. & Mulholland, A. J., 28 Feb 2012, In: Biochemistry. 51, 8, p. 1774-1786 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

61 Citations (Scopus)

Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions

Lonsdale, R., Harvey, J. N. & Mulholland, A. J., Nov 2012, In: Journal of Chemical Theory and Computation. 8, 11, p. 4637-4645 9 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

90 Citations (Scopus)

Long Time Scale GPU Dynamics Reveal the Mechanism of Drug Resistance of the Dual Mutant I223R/H275Y Neuraminidase from H1N1-2009 Influenza Virus

Woods, C. J., Malaisree, M., Pattarapongdilok, N., Sompornpisut, P., Hannongbua, S. & Mulholland, A. J., 29 May 2012, In: Biochemistry. 51, 21, p. 4364-4375 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

34 Citations (Scopus)

Mechanism of C-terminal intein cleavage in protein splicing from QM/MM molecular dynamics simulations

Mujika, J. I., Lopez, X. & Mulholland, A. J., 14 Feb 2012, In: Organic and Biomolecular Chemistry. 10, 6, p. 1207-18 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

31 Citations (Scopus)

Protein dynamics and enzyme catalysis: the ghost in the machine?

Glowacki, D. R., Harvey, J. N. & Mulholland, A. J., Jun 2012, In: Biochemical Society Transactions. 40, p. 515-521 7 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

20 Citations (Scopus)

Taking Ockham's razor to enzyme dynamics and catalysis

Glowacki, D. R., Harvey, J. N. & Mulholland, A. J., Jan 2012, In: Nature Chemistry. 4, p. 169-176 8 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

223 Citations (Scopus)

The Basis for Carbapenem Hydrolysis by Class A β-Lactamases: A Combined Investigation using Crystallography and Simulations.

Fonseca, M. F., Chudyk, E. I., Van der Kamp, M. W., Correia, A., Mulholland, A. J. & Spencer, J., 7 Nov 2012, In: Journal of the American Chemical Society. 134, 44, p. 18275-18285 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

76 Citations (Scopus)

CCP-BioSim: Biomolecular simulation at the life sciences interface

Research output

Search results