| Year |
Citation |
Score |
| 2023 |
Castelli M, Marchetti F, Osuna S, F Oliveira AS, Mulholland AJ, Serapian SA, Colombo G. Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary Approaches Based on Unbiased Molecular Dynamics Simulations. Journal of the American Chemical Society. 146: 901-919. PMID 38116743 DOI: 10.1021/jacs.3c11396 |
0.71 |
|
| 2023 |
Deeks HM, Zinovjev K, Barnoud J, Mulholland AJ, van der Kamp MW, Glowacki DR. Free energy along drug-protein binding pathways interactively sampled in virtual reality. Scientific Reports. 13: 16665. PMID 37794083 DOI: 10.1038/s41598-023-43523-x |
0.738 |
|
| 2023 |
Tooke CL, Hinchliffe P, Beer M, Zinovjev K, Colenso CK, Schofield CJ, Mulholland AJ, Spencer J. Tautomer-Specific Deacylation and Ω-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 β-Lactamase. Journal of the American Chemical Society. PMID 36972204 DOI: 10.1021/jacs.2c12123 |
0.359 |
|
| 2022 |
Chudyk EI, Beer M, Limb MAL, Jones CA, Spencer J, van der Kamp MW, Mulholland AJ. QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-Lactamases. Acs Infectious Diseases. PMID 35877936 DOI: 10.1021/acsinfecdis.2c00152 |
0.782 |
|
| 2022 |
Hirvonen VHA, Weizmann TM, Mulholland AJ, Spencer J, van der Kamp MW. Multiscale Simulations Identify Origins of Differential Carbapenem Hydrolysis by the OXA-48 β-Lactamase. Acs Catalysis. 12: 4534-4544. PMID 35571461 DOI: 10.1021/acscatal.1c05694 |
0.787 |
|
| 2022 |
Haldar S, Zhang Y, Xia Y, Islam B, Liu S, Gervasio FL, Mulholland AJ, Waller ZAE, Wei D, Haider S. Mechanistic Insights into the Ligand-Induced Unfolding of an RNA G-Quadruplex. Journal of the American Chemical Society. PMID 34989224 DOI: 10.1021/jacs.1c11248 |
0.561 |
|
| 2021 |
Yang Z, Twidale RM, Gervasoni S, Suardíaz R, Colenso CK, Lang EJM, Spencer J, Mulholland AJ. Multiscale Workflow for Modeling Ligand Complexes of Zinc Metalloproteins. Journal of Chemical Information and Modeling. PMID 34748329 DOI: 10.1021/acs.jcim.1c01109 |
0.745 |
|
| 2021 |
Twidale RM, Hinchliffe P, Spencer J, Mulholland AJ. Crystallography and QM/MM Simulations Identify Preferential Binding of Hydrolyzed Carbapenem and Penem Antibiotics to the L1 Metallo-β-Lactamase in the Imine Form. Journal of Chemical Information and Modeling. PMID 34637298 DOI: 10.1021/acs.jcim.1c00663 |
0.302 |
|
| 2021 |
Hindson SA, Bunzel HA, Frank B, Svistunenko DA, Williams C, van der Kamp MW, Mulholland AJ, Pudney CR, Anderson JLR. Rigidifying a Enzyme Increases Activity and Induces a Negative Activation Heat Capacity. Acs Catalysis. 11: 11532-11541. PMID 34557328 DOI: 10.1021/acscatal.1c01776 |
0.765 |
|
| 2021 |
Bunzel HA, Anderson JLR, Hilvert D, Arcus VL, van der Kamp MW, Mulholland AJ. Evolution of dynamical networks enhances catalysis in a designer enzyme. Nature Chemistry. PMID 34413499 DOI: 10.1038/s41557-021-00763-6 |
0.756 |
|
| 2021 |
Voice AT, Tresadern G, Twidale RM, van Vlijmen H, Mulholland AJ. Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations. Chemical Science. 12: 5511-5516. PMID 33995994 DOI: 10.1039/d0sc06122k |
0.675 |
|
| 2021 |
Jenkins JMX, Noble CEM, Grayson KJ, Mulholland AJ, Anderson JLR. Substrate promiscuity of a de novo designed peroxidase. Journal of Inorganic Biochemistry. 217: 111370. PMID 33621939 DOI: 10.1016/j.jinorgbio.2021.111370 |
0.308 |
|
| 2021 |
Suardíaz R, Lythell E, Hinchliffe P, van der Kamp M, Spencer J, Fey N, Mulholland AJ. Catalytic mechanism of the colistin resistance protein MCR-1. Organic & Biomolecular Chemistry. PMID 33606866 DOI: 10.1039/d0ob02566f |
0.789 |
|
| 2020 |
O'Hagan MP, Haldar S, Morales JC, Mulholland AJ, Galan MC. Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands. Chemical Science. 12: 1415-1426. PMID 34163904 DOI: 10.1039/d0sc05223j |
0.581 |
|
| 2020 |
Phintha A, Prakinee K, Jaruwat A, Lawan N, Visitsatthawong S, Kantiwiriyawanitch C, Songsungthong W, Trisrivirat D, Chenprakhon P, Mulholland A, van Pée KH, Chitnumsub P, Chaiyen P. Dissecting the low catalytic capability of flavin-dependent halogenases. The Journal of Biological Chemistry. 296: 100068. PMID 33465708 DOI: 10.1074/jbc.RA120.016004 |
0.312 |
|
| 2020 |
Tooke CL, Hinchliffe P, Bonomo RA, Schofield CJ, Mulholland AJ, Spencer J. Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl-enzyme conformational dynamics to extend antibiotic resistance. The Journal of Biological Chemistry. PMID 33257320 DOI: 10.1074/jbc.RA120.016461 |
0.364 |
|
| 2020 |
Arcus VL, van der Kamp MW, Pudney CR, Mulholland AJ. Enzyme evolution and the temperature dependence of enzyme catalysis. Current Opinion in Structural Biology. 65: 96-101. PMID 32659635 DOI: 10.1016/j.sbi.2020.06.001 |
0.77 |
|
| 2020 |
Douglas-Gallardo OA, Shepherd I, Bennie SJ, Ranaghan KE, Mulholland AJ, Vöhringer-Martinez E. Electronic structure benchmark calculations of CO fixing elementary chemical steps in RuBisCO using the projector-based embedding approach. Journal of Computational Chemistry. PMID 32640497 DOI: 10.1002/jcc.26380 |
0.328 |
|
| 2020 |
Lythell E, Suardíaz R, Hinchliffe P, Hanpaibool C, Visitsatthawong S, Oliveira ASF, Lang EJM, Surawatanawong P, Lee VS, Rungrotmongkol T, Fey N, Spencer J, Mulholland AJ. Resistance to the "last resort" antibiotic colistin: a single-zinc mechanism for phosphointermediate formation in MCR enzymes. Chemical Communications (Cambridge, England). PMID 32432618 DOI: 10.1039/D0Cc02520H |
0.754 |
|
| 2020 |
O'Hagan MP, Ramos-Soriano J, Haldar S, Sheikh S, Morales JC, Mulholland AJ, Galan MC. Visible-light photoswitching of ligand binding mode suggests G-quadruplex DNA as a target for photopharmacology. Chemical Communications (Cambridge, England). PMID 32267261 DOI: 10.1039/D0Cc01581D |
0.526 |
|
| 2020 |
Kwon H, Basran J, Devos JM, Suardíaz R, van der Kamp MW, Mulholland AJ, Schrader TE, Ostermann A, Blakeley MP, Moody PCE, Raven EL. Visualizing the protons in a metalloenzyme electron proton transfer pathway. Proceedings of the National Academy of Sciences of the United States of America. PMID 32152099 DOI: 10.1073/pnas.1918936117 |
0.767 |
|
| 2020 |
Jagger BR, Kochanek SE, Haldar S, Amaro RE, Mulholland AJ. Multiscale simulation approaches to modeling drug-protein binding. Current Opinion in Structural Biology. 61: 213-221. PMID 32113133 DOI: 10.1016/J.Sbi.2020.01.014 |
0.589 |
|
| 2020 |
Arcus VL, Mulholland AJ. Temperature, Dynamics, and Enzyme-Catalyzed Reaction Rates. Annual Review of Biophysics. PMID 32040931 DOI: 10.1146/annurev-biophys-121219-081520 |
0.335 |
|
| 2019 |
Leferink NGH, Ranaghan KE, Battye J, Johannissen LO, Hay S, van der Kamp MW, Mulholland AJ, Scrutton NS. Taming the Reactivity of Monoterpene Synthases To Guide Regioselective Product Hydroxylation. Chembiochem : a European Journal of Chemical Biology. PMID 31682055 DOI: 10.1002/cbic.201900672 |
0.747 |
|
| 2019 |
Kamsri P, Punkvang A, Hannongbua S, Suttisintong K, Kittakoop P, Spencer J, Mulholland AJ, Pungpo P. In silico study directed towards identification of the key structural features of GyrB inhibitors targeting MTB DNA gyrase: HQSAR, CoMSIA and molecular dynamics simulations. Sar and Qsar in Environmental Research. 30: 775-800. PMID 31607177 DOI: 10.1080/1062936X.2019.1658218 |
0.301 |
|
| 2019 |
Kiani YS, Ranaghan KE, Jabeen I, Mulholland AJ. Molecular Dynamics Simulation Framework to Probe the Binding Hypothesis of CYP3A4 Inhibitors. International Journal of Molecular Sciences. 20. PMID 31510073 DOI: 10.3390/ijms20184468 |
0.309 |
|
| 2019 |
Voice A, Tresadern G, Van Vlijmen H, Mulholland AJ. Limitations of ligand-only approaches for predicting the reactivity of covalent inhibitors. Journal of Chemical Information and Modeling. PMID 31498988 DOI: 10.1021/Acs.Jcim.9B00404 |
0.675 |
|
| 2019 |
Hirvonen V, Hammond K, Chudyk EI, Limb M, Spencer J, Mulholland AJ, van der Kamp MW. An efficient computational assay for β-lactam antibiotic breakdown by class A β-lactamases. Journal of Chemical Information and Modeling. PMID 31361944 DOI: 10.1021/acs.jcim.9b00442 |
0.726 |
|
| 2019 |
Nutho B, Mulholland AJ, Rungrotmongkol T. The reaction mechanism of Zika virus NS2B/NS3 serine protease inhibition by dipeptidyl aldehyde: a QM/MM study. Physical Chemistry Chemical Physics : Pccp. 21: 14945-14956. PMID 31236554 DOI: 10.1039/c9cp02377a |
0.3 |
|
| 2019 |
Leferink NGH, Ranaghan KE, Karuppiah V, Currin A, van der Kamp MW, Mulholland AJ, Scrutton NS. Experiment and Simulation Reveal How Mutations in Functional Plasticity Regions Guide Plant Monoterpene Synthase Product Outcome. Acs Catalysis. 8: 3780-3791. PMID 31157124 DOI: 10.1021/acscatal.8b00692 |
0.756 |
|
| 2019 |
Raza S, Ranaghan KE, van der Kamp MW, Woods CJ, Mulholland AJ, Azam SS. Visualizing protein-ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site. Journal of Computer-Aided Molecular Design. PMID 30989572 DOI: 10.1007/s10822-019-00200-4 |
0.735 |
|
| 2019 |
Nutho B, Mulholland AJ, Rungrotmongkol T. Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate. The Journal of Physical Chemistry. B. 123: 2889-2903. PMID 30845796 DOI: 10.1021/acs.jpcb.9b02157 |
0.35 |
|
| 2019 |
Punkvang A, Kamsri P, Mulholland A, Spencer J, Hannongbua S, Pungpo P. Simulations of Shikimate Dehydrogenase from Mycobacterium tuberculosis in Complex with 3-Dehydroshikimate and NADPH Suggest Strategies for MtbSDH Inhibition. Journal of Chemical Information and Modeling. PMID 30840825 DOI: 10.1021/Acs.Jcim.8B00834 |
0.391 |
|
| 2019 |
O'Hagan M, Haldar S, Duchi M, Oliver T, Mulholland A, Morales JC, Galan MC. A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Conformational Unfolding of G-Quadruplex DNA. Angewandte Chemie (International Ed. in English). PMID 30682233 DOI: 10.1002/Anie.201900740 |
0.533 |
|
| 2019 |
Nutho B, Mulholland A, Rungrotmongkol T. QM/MM Study on Cleavage Mechanism Catalyzed by Zika Virus NS2B/NS3 Serine Protease Biophysical Journal. 116: 559a. DOI: 10.1016/J.Bpj.2018.11.3005 |
0.304 |
|
| 2018 |
Ainsley J, Mulholland AJ, Black GW, Sparagano O, Christov CZ, Karabencheva-Christova TG. Structural Insights from Molecular Dynamics Simulations of Tryptophan 7-Halogenase and Tryptophan 5-Halogenase. Acs Omega. 3: 4847-4859. PMID 31458701 DOI: 10.1021/acsomega.8b00385 |
0.348 |
|
| 2018 |
Liao Q, Kulkarni Y, Sengupta U, Petrović D, Mulholland AJ, van der Kamp MW, Strodel B, Kamerlin SCL. Loop Motion in Triosephosphate Isomerase is not a Simple Open and Shut Case. Journal of the American Chemical Society. PMID 30362343 DOI: 10.1021/Jacs.8B09378 |
0.768 |
|
| 2018 |
Limb MAL, Suardiaz R, Grant IM, Mulholland AJ. QM/MM Simulations Show Saccharide Distortion is Required for Reaction in Hen Egg-White Lysozyme. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 30347479 DOI: 10.1002/chem.201805250 |
0.781 |
|
| 2018 |
Haldar S, Comitani F, Saladino G, Woods C, van der Kamp MW, Mulholland AJ, Gervasio FL. A Multiscale Simulation Approach to Modelling Drug-Protein Binding Kinetics. Journal of Chemical Theory and Computation. PMID 30208708 DOI: 10.1021/Acs.Jctc.8B00687 |
0.795 |
|
| 2018 |
Ainsley J, Lodola A, Mulholland AJ, Christov CZ, Karabencheva-Christova TG. Combined Quantum Mechanics and Molecular Mechanics Studies of Enzymatic Reaction Mechanisms. Advances in Protein Chemistry and Structural Biology. 113: 1-32. PMID 30149903 DOI: 10.1016/bs.apcsb.2018.07.001 |
0.352 |
|
| 2018 |
Fritz R, Alzate-Morales JH, Spencer J, Mulholland AJ, van der Kamp MW. Multiscale simulations of clavulanate inhibition identify the reactive complex in class A β-lactamases and predict efficiency of inhibition. Biochemistry. PMID 29812917 DOI: 10.1021/acs.biochem.8b00480 |
0.763 |
|
| 2018 |
Lence E, van der Kamp MW, González-Bello C, Mulholland AJ. QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes. Organic & Biomolecular Chemistry. PMID 29767194 DOI: 10.1039/c8ob00066b |
0.785 |
|
| 2018 |
Callegari D, Ranaghan KE, Woods CJ, Minari R, Tiseo M, Mor M, Mulholland AJ, Lodola A. L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib. Chemical Science. 9: 2740-2749. PMID 29732058 DOI: 10.1039/C7Sc04761D |
0.364 |
|
| 2018 |
van der Kamp MW, Prentice EJ, Kraakman KL, Connolly M, Mulholland AJ, Arcus VL. Dynamical origins of heat capacity changes in enzyme-catalysed reactions. Nature Communications. 9: 1177. PMID 29563521 DOI: 10.1038/s41467-018-03597-y |
0.776 |
|
| 2018 |
Messiha HL, Ahmed ST, Karuppiah V, Suardiaz R, Ascue Avalos GA, Fey N, Yeates S, Toogood HS, Mulholland AJ, Scrutton NS. Biocatalytic Routes to Lactone Monomers for Polymer Production. Biochemistry. PMID 29533655 DOI: 10.1021/Acs.Biochem.8B00169 |
0.718 |
|
| 2018 |
Zhang X, Bennie SJ, van der Kamp MW, Glowacki DR, Manby FR, Mulholland AJ. Multiscale analysis of enantioselectivity in enzyme-catalysed 'lethal synthesis' using projector-based embedding. Royal Society Open Science. 5: 171390. PMID 29515856 DOI: 10.1098/Rsos.171390 |
0.773 |
|
| 2017 |
Karabencheva-Christova TG, Torras J, Mulholland AJ, Lodola A, Christov CZ. Mechanistic Insights into the Reaction of Chlorination of Tryptophan Catalyzed by Tryptophan 7-Halogenase. Scientific Reports. 7: 17395. PMID 29234124 DOI: 10.1038/s41598-017-17789-x |
0.366 |
|
| 2017 |
Jitonnom J, Mujika JI, van der Kamp MW, Mulholland AJ. Quantum Mechanics/Molecular Mechanics Simulations Identify the Ring-Opening Mechanism of Creatininase. Biochemistry. 56: 6377-6388. PMID 29140090 DOI: 10.1021/Acs.Biochem.7B01032 |
0.806 |
|
| 2017 |
Ge Y, van der Kamp M, Malaisree M, Liu D, Liu Y, Mulholland AJ. Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations. Journal of Computer-Aided Molecular Design. PMID 28994029 DOI: 10.1007/s10822-017-0073-y |
0.746 |
|
| 2017 |
Karuppiah V, Ranaghan KE, Leferink NGH, Johannissen LO, Shanmugam M, Ní Cheallaigh A, Bennett NJ, Kearsey LJ, Takano E, Gardiner JM, van der Kamp MW, Hay S, Mulholland AJ, Leys D, Scrutton NS. Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase. Acs Catalysis. 7: 6268-6282. PMID 28966840 DOI: 10.1021/Acscatal.7B01924 |
0.758 |
|
| 2017 |
Ranaghan KE, Morris WG, Masgrau L, Senthilkumar K, Johannissen LO, Scrutton NS, Harvey JN, Manby FR, Mulholland AJ. Ab Initio QM/MM Modelling of the Rate-Limiting Proton Transfer Step in the Deamination of Tryptamine by Aromatic Amine Dehydrogenase. The Journal of Physical Chemistry. B. PMID 28930453 DOI: 10.1021/Acs.Jpcb.7B06892 |
0.39 |
|
| 2017 |
Watkins DW, Jenkins JMX, Grayson KJ, Wood N, Steventon JW, Le Vay KK, Goodwin MI, Mullen AS, Bailey HJ, Crump MP, MacMillan F, Mulholland AJ, Cameron G, Sessions RB, Mann S, et al. Construction and in vivo assembly of a catalytically proficient and hyperthermostable de novo enzyme. Nature Communications. 8: 358. PMID 28842561 DOI: 10.1038/S41467-017-00541-4 |
0.335 |
|
| 2017 |
Beker W, van der Kamp MW, Mulholland AJ, Sokalski WA. Rapid Estimation of Catalytic Efficiency by Cumulative Atomic Multipole Moments: Application to Ketosteroid Isomerase Mutants. Journal of Chemical Theory and Computation. 13: 945-955. PMID 28103023 DOI: 10.1021/acs.jctc.6b01131 |
0.739 |
|
| 2016 |
Bennie SJ, van der Kamp MW, Pennifold RC, Stella M, Manby FR, Mulholland AJ. A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase. Journal of Chemical Theory and Computation. 12: 2689-97. PMID 27159381 DOI: 10.1021/Acs.Jctc.6B00285 |
0.761 |
|
| 2016 |
Byrne MJ, Lees NR, Han LC, van der Kamp MW, Mulholland AJ, Stach JE, Willis CL, Race PR. The Catalytic Mechanism of a Natural Diels-Alderase Revealed in Molecular Detail. Journal of the American Chemical Society. PMID 27140661 DOI: 10.1021/Jacs.6B00232 |
0.777 |
|
| 2016 |
Arcus VL, Prentice EJ, Hobbs JK, Mulholland AJ, van der Kamp MW, Pudney CR, Parker EJ, Schipper LA. On the Temperature Dependence of Enzyme-catalyzed Rates. Biochemistry. PMID 26881922 DOI: 10.1021/Acs.Biochem.5B01094 |
0.766 |
|
| 2015 |
Kaiyawet N, Lonsdale R, Rungrotmongkol T, Mulholland AJ, Hannongbua S. High-level QM/MM calculations support the concerted mechanism for Michael addition and covalent complex formation in thymidylate synthase. Journal of Chemical Theory and Computation. 11: 713-22. PMID 26579604 DOI: 10.1021/Ct5005033 |
0.311 |
|
| 2015 |
Wells SA, van der Kamp MW, McGeagh JD, Mulholland AJ. Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions. Plos One. 10: e0133372. PMID 26241964 DOI: 10.1371/journal.pone.0133372 |
0.755 |
|
| 2014 |
Mlýnský V, Banáš P, Šponer J, van der Kamp MW, Mulholland AJ, Otyepka M. Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. Journal of Chemical Theory and Computation. 10: 1608-22. PMID 26580373 DOI: 10.1021/Ct401015E |
0.764 |
|
| 2014 |
Lever G, Cole DJ, Lonsdale R, Ranaghan KE, Wales DJ, Mulholland AJ, Skylaris CK, Payne MC. Large-Scale Density Functional Theory Transition State Searching in Enzymes. The Journal of Physical Chemistry Letters. 5: 3614-9. PMID 26278727 DOI: 10.1021/Jz5018703 |
0.306 |
|
| 2014 |
Chudyk EI, Limb MA, Jones C, Spencer J, van der Kamp MW, Mulholland AJ. QM/MM simulations as an assay for carbapenemase activity in class A β-lactamases. Chemical Communications (Cambridge, England). 50: 14736-9. PMID 25321894 DOI: 10.1039/c4cc06495j |
0.76 |
|
| 2014 |
Jitonnom J, Limb MA, Mulholland AJ. QM/MM free-energy simulations of reaction in Serratia marcescens Chitinase B reveal the protonation state of Asp142 and the critical role of Tyr214. The Journal of Physical Chemistry. B. 118: 4771-83. PMID 24730355 DOI: 10.1021/Jp500652X |
0.772 |
|
| 2014 |
Daniels AD, Campeotto I, van der Kamp MW, Bolt AH, Trinh CH, Phillips SE, Pearson AR, Nelson A, Mulholland AJ, Berry A. Reaction mechanism of N-acetylneuraminic acid lyase revealed by a combination of crystallography, QM/MM simulation, and mutagenesis. Acs Chemical Biology. 9: 1025-32. PMID 24521460 DOI: 10.1021/Cb500067Z |
0.789 |
|
| 2014 |
Román-Meléndez GD, von Glehn P, Harvey JN, Mulholland AJ, Marsh EN. Role of active site residues in promoting cobalt-carbon bond homolysis in adenosylcobalamin-dependent mutases revealed through experiment and computation. Biochemistry. 53: 169-77. PMID 24341954 DOI: 10.1021/Bi4012644 |
0.311 |
|
| 2014 |
Ranaghan KE, Hung JE, Bartlett GJ, Mooibroek TJ, Harvey JN, Woolfson DN, Van Der Donk WA, Mulholland AJ. A catalytic role for methionine revealed by a combination of computation and experiments on phosphite dehydrogenase Chemical Science. 5: 2191-2199. DOI: 10.1039/C3Sc53009D |
0.394 |
|
| 2014 |
Lawan N, Ranaghan KE, Manby FR, Mulholland AJ. Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase Chemical Physics Letters. 608: 380-385. DOI: 10.1016/J.Cplett.2014.06.010 |
0.357 |
|
| 2013 |
van der Kamp MW, Sirirak J, Żurek J, Allemann RK, Mulholland AJ. Conformational change and ligand binding in the aristolochene synthase catalytic cycle. Biochemistry. 52: 8094-105. PMID 24106830 DOI: 10.1021/Bi400898K |
0.774 |
|
| 2013 |
Luk LY, Javier Ruiz-PernÃa J, Dawson WM, Roca M, Loveridge EJ, Glowacki DR, Harvey JN, Mulholland AJ, Tuñón I, Moliner V, Allemann RK. Unraveling the role of protein dynamics in dihydrofolate reductase catalysis. Proceedings of the National Academy of Sciences of the United States of America. 110: 16344-9. PMID 24065822 DOI: 10.1073/Pnas.1312437110 |
0.381 |
|
| 2013 |
Chudyk EI, Dyguda-Kazimierowicz E, Langner KM, Sokalski WA, Lodola A, Mor M, Sirirak J, Mulholland AJ. Nonempirical energetic analysis of reactivity and covalent inhibition of fatty acid amide hydrolase. The Journal of Physical Chemistry. B. 117: 6656-66. PMID 23654226 DOI: 10.1021/jp401834v |
0.346 |
|
| 2013 |
van der Kamp MW, Mulholland AJ. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry. 52: 2708-28. PMID 23557014 DOI: 10.1021/bi400215w |
0.783 |
|
| 2013 |
Christov CZ, Lodola A, Karabencheva-Christova TG, Wan S, Coveney PV, Mulholland AJ. Conformational effects on the pro-S hydrogen abstraction reaction in cyclooxygenase-1: an integrated QM/MM and MD study. Biophysical Journal. 104: L5-7. PMID 23473504 DOI: 10.1016/j.bpj.2013.01.040 |
0.337 |
|
| 2013 |
van der Kamp MW, Chaudret R, Mulholland AJ. QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis. The Febs Journal. 280: 3120-31. PMID 23356661 DOI: 10.1111/Febs.12158 |
0.797 |
|
| 2013 |
Lodola A, Mulholland AJ. Computational enzymology. Methods in Molecular Biology (Clifton, N.J.). 924: 67-89. PMID 23034746 DOI: 10.1007/978-1-62703-017-5_4 |
0.305 |
|
| 2012 |
Fonseca F, Chudyk EI, van der Kamp MW, Correia A, Mulholland AJ, Spencer J. The basis for carbapenem hydrolysis by class A β-lactamases: a combined investigation using crystallography and simulations. Journal of the American Chemical Society. 134: 18275-85. PMID 23030300 DOI: 10.1021/ja304460j |
0.754 |
|
| 2012 |
Glowacki DR, Harvey JN, Mulholland AJ. Protein dynamics and enzyme catalysis: the ghost in the machine? Biochemical Society Transactions. 40: 515-21. PMID 22616861 DOI: 10.1042/Bst20120047 |
0.351 |
|
| 2012 |
Glowacki DR, Harvey JN, Mulholland AJ. Taking Ockham's razor to enzyme dynamics and catalysis. Nature Chemistry. 4: 169-76. PMID 22354430 DOI: 10.1038/Nchem.1244 |
0.314 |
|
| 2012 |
Lonsdale R, Hoyle S, Grey DT, Ridder L, Mulholland AJ. Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling. Biochemistry. 51: 1774-86. PMID 22280021 DOI: 10.1021/Bi201722J |
0.388 |
|
| 2012 |
Lonsdale R, Harvey JN, Mulholland AJ. A practical guide to modelling enzyme-catalysed reactions. Chemical Society Reviews. 41: 3025-38. PMID 22278388 DOI: 10.1039/C2Cs15297E |
0.349 |
|
| 2012 |
Mujika JI, Lopez X, Mulholland AJ. Mechanism of C-terminal intein cleavage in protein splicing from QM/MM molecular dynamics simulations. Organic & Biomolecular Chemistry. 10: 1207-18. PMID 22179261 DOI: 10.1039/c1ob06444d |
0.36 |
|
| 2012 |
Jitonnom J, Mulholland AJ. Insights into conformational changes of procarboxypeptidase A and B from simulations: a plausible explanation for different intrinsic activity Theoretical Chemistry Accounts. 131. DOI: 10.1007/S00214-012-1224-9 |
0.724 |
|
| 2011 |
van der Kamp MW, McGeagh JD, Mulholland AJ. "Lethal synthesis" of fluorocitrate by citrate synthase explained through QM/MM modeling. Angewandte Chemie (International Ed. in English). 50: 10349-51. PMID 21922613 DOI: 10.1002/anie.201103260 |
0.712 |
|
| 2011 |
Jitonnom J, Lee VS, Nimmanpipug P, Rowlands HA, Mulholland AJ. Quantum mechanics/molecular mechanics modeling of substrate-assisted catalysis in family 18 chitinases: conformational changes and the role of Asp142 in catalysis in ChiB. Biochemistry. 50: 4697-711. PMID 21469745 DOI: 10.1021/Bi101362G |
0.77 |
|
| 2011 |
Oláh J, Mulholland AJ, Harvey JN. Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450 Proceedings of the National Academy of Sciences of the United States of America. 108: 6050-6055. PMID 21444768 DOI: 10.1073/Pnas.1010194108 |
0.301 |
|
| 2011 |
Capoferri L, Mor M, Sirirak J, Chudyk E, Mulholland AJ, Lodola A. Application of a SCC-DFTB QM/MM approach to the investigation of the catalytic mechanism of fatty acid amide hydrolase. Journal of Molecular Modeling. 17: 2375-83. PMID 21365225 DOI: 10.1007/s00894-011-0981-z |
0.346 |
|
| 2011 |
Claeyssens F, Ranaghan KE, Lawan N, MacRae SJ, Manby FR, Harvey JN, Mulholland AJ. Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions Organic and Biomolecular Chemistry. 9: 1578-1590. PMID 21243152 DOI: 10.1039/C0Ob00691B |
0.394 |
|
| 2011 |
McGeagh JD, Ranaghan KE, Mulholland AJ. Protein dynamics and enzyme catalysis: insights from simulations. Biochimica Et Biophysica Acta. 1814: 1077-92. PMID 21167324 DOI: 10.1016/j.bbapap.2010.12.002 |
0.324 |
|
| 2011 |
Lonsdale R, Harvey JN, Manby FR, Mulholland AJ. Comment on "a stationary-wave model of enzyme catalysis" by Carlo Canepa Journal of Computational Chemistry. 32: 368-369. PMID 20652884 DOI: 10.1002/Jcc.21618 |
0.377 |
|
| 2010 |
Lodola A, Sirirak J, Fey N, Rivara S, Mor M, Mulholland AJ. Structural Fluctuations in Enzyme-Catalyzed Reactions: Determinants of Reactivity in Fatty Acid Amide Hydrolase from Multivariate Statistical Analysis of Quantum Mechanics/Molecular Mechanics Paths. Journal of Chemical Theory and Computation. 6: 2948-60. PMID 26616091 DOI: 10.1021/Ct100264J |
0.372 |
|
| 2010 |
van der Kamp MW, Zurek J, Manby FR, Harvey JN, Mulholland AJ. Testing high-level QM/MM methods for modeling enzyme reactions: acetyl-CoA deprotonation in citrate synthase. The Journal of Physical Chemistry. B. 114: 11303-14. PMID 20690673 DOI: 10.1021/Jp104069T |
0.773 |
|
| 2010 |
Ranaghan KE, Mulholland AJ. Computer simulations of quantum tunnelling in enzyme-catalysed hydrogen transfer reactions. Interdisciplinary Sciences, Computational Life Sciences. 2: 78-97. PMID 20640799 DOI: 10.1007/s12539-010-0093-y |
0.363 |
|
| 2010 |
Lonsdale R, Harvey JN, Mulholland AJ. Compound I reactivity defines alkene oxidation selectivity in cytochrome P450cam. The Journal of Physical Chemistry. B. 114: 1156-62. PMID 20014756 DOI: 10.1021/Jp910127J |
0.332 |
|
| 2010 |
Ranaghan KE, Mulholland AJ. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods International Reviews in Physical Chemistry. 29: 65-133. DOI: 10.1080/01442350903495417 |
0.33 |
|
| 2010 |
Lodola A, Sirirak J, Fey N, Rivara S, Mor M, Mulholland AJ. Structural fluctuations in enzyme-catalyzed reactions: Determinants of Reactivity in fatty acid amide hydrolase from multivariate statistical analysis of quantum mechanics/molecular mechanics paths Journal of Chemical Theory and Computation. 6: 2948-2960. DOI: 10.1021/ct100264j |
0.308 |
|
| 2010 |
Ren Q, Ranaghan KE, Mulholland AJ, Harvey JN, Manby FR, Balint-Kurti GG. Optimal control design of laser pulses for mode specific vibrational excitation in an enzyme-substrate complex Chemical Physics Letters. 491: 230-236. DOI: 10.1016/J.Cplett.2010.03.089 |
0.546 |
|
| 2009 |
Hermann JC, Pradon J, Harvey JN, Mulholland AJ. High level QM/MM modeling of the formation of the tetrahedral intermediate in the acylation of wild type and K73A mutant TEM-1 class A beta-lactamase. The Journal of Physical Chemistry. A. 113: 11984-94. PMID 19791786 DOI: 10.1021/Jp9037254 |
0.329 |
|
| 2009 |
Mujika JI, Lopez X, Mulholland AJ. Modeling protein splicing: reaction pathway for C-terminal splice and intein scission. The Journal of Physical Chemistry. B. 113: 5607-16. PMID 19326906 DOI: 10.1021/jp808911p |
0.328 |
|
| 2009 |
Szeto MWY, Mujika JI, Zurek J, Mulholland AJ, Harvey JN. QM/MM study on the mechanism of peptide hydrolysis by carboxypeptidase A Journal of Molecular Structure: Theochem. 898: 106-114. DOI: 10.1016/J.Theochem.2008.06.033 |
0.325 |
|
| 2008 |
van der Kamp MW, Mulholland AJ. Computational enzymology: insight into biological catalysts from modelling. Natural Product Reports. 25: 1001-14. PMID 19030602 DOI: 10.1039/b600517a |
0.789 |
|
| 2008 |
Bowman AL, Grant IM, Mulholland AJ. QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate. Chemical Communications (Cambridge, England). 4425-7. PMID 18802578 DOI: 10.1039/b810099c |
0.386 |
|
| 2008 |
van der Kamp MW, Shaw KE, Woods CJ, Mulholland AJ. Biomolecular simulation and modelling: status, progress and prospects. Journal of the Royal Society, Interface / the Royal Society. 5: S173-90. PMID 18611844 DOI: 10.1098/rsif.2008.0105.focus |
0.735 |
|
| 2008 |
van der Kamp MW, Perruccio F, Mulholland AJ. High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase. Chemical Communications (Cambridge, England). 1874-6. PMID 18401503 DOI: 10.1039/b800496j |
0.78 |
|
| 2008 |
Smith LJ, Browne S, Mulholland AJ, Mantle TJ. Computational and experimental studies on the catalytic mechanism of biliverdin-IXbeta reductase. The Biochemical Journal. 411: 475-84. PMID 18241201 DOI: 10.1042/BJ20071495 |
0.324 |
|
| 2008 |
Mulholland AJ. Computational enzymology: modelling the mechanisms of biological catalysts. Biochemical Society Transactions. 36: 22-6. PMID 18208378 DOI: 10.1042/BST0360022 |
0.339 |
|
| 2008 |
Pentikäinen U, Pentikäinen OT, Mulholland AJ. Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations. Proteins. 70: 498-508. PMID 17705275 DOI: 10.1002/prot.21540 |
0.341 |
|
| 2007 |
RodrÃguez A, Oliva C, González M, van der Kamp M, Mulholland AJ. Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate. The Journal of Physical Chemistry. B. 111: 12909-15. PMID 17935316 DOI: 10.1021/jp0743469 |
0.771 |
|
| 2007 |
Mulholland AJ. Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions. Chemistry Central Journal. 1: 19. PMID 17880750 DOI: 10.1186/1752-153X-1-19 |
0.367 |
|
| 2007 |
Ranaghan KE, Masgrau L, Scrutton NS, Sutcliffe MJ, Mulholland AJ. Analysis of classical and quantum paths for deprotonation of methylamine by methylamine dehydrogenase. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 8: 1816-35. PMID 17676581 DOI: 10.1002/CPHC.200700143 |
0.387 |
|
| 2007 |
van der Kamp MW, Perruccio F, Mulholland AJ. Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl-CoA enolization in citrate synthase. Proteins. 69: 521-35. PMID 17623847 DOI: 10.1002/prot.21482 |
0.767 |
|
| 2007 |
van der Kamp MW, Perruccio F, Mulholland AJ. Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase. Journal of Molecular Graphics & Modelling. 26: 676-90. PMID 17493853 DOI: 10.1016/J.JMGM.2007.04.002 |
0.776 |
|
| 2007 |
Bowman AL, Ridder L, Rietjens IM, Vervoort J, Mulholland AJ. Molecular determinants of xenobiotic metabolism: QM/MM simulation of the conversion of 1-chloro-2,4-dinitrobenzene catalyzed by M1-1 glutathione S-transferase. Biochemistry. 46: 6353-63. PMID 17480056 DOI: 10.1021/bi0622827 |
0.376 |
|
| 2007 |
Masgrau L, Ranaghan KE, Scrutton NS, Mulholland AJ, Sutcliffe MJ. Tunneling and classical paths for proton transfer in an enzyme reaction dominated by tunneling: oxidation of tryptamine by aromatic amine dehydrogenase. The Journal of Physical Chemistry. B. 111: 3032-47. PMID 17388439 DOI: 10.1021/JP067898K |
0.381 |
|
| 2007 |
Lodola A, Mor M, Zurek J, Tarzia G, Piomelli D, Harvey JN, Mulholland AJ. Conformational effects in enzyme catalysis: reaction via a high energy conformation in fatty acid amide hydrolase. Biophysical Journal. 92: L20-2. PMID 17098788 DOI: 10.1529/Biophysj.106.098434 |
0.389 |
|
| 2007 |
Bowman A, Mulholland A. Simulating Enzyme-Catalyzed Reactions Cheminform. 38. DOI: 10.1002/chin.200748261 |
0.341 |
|
| 2006 |
Zurek J, Foloppe N, Harvey JN, Mulholland AJ. Mechanisms of reaction in cytochrome P450: Hydroxylation of camphor in P450cam. Organic & Biomolecular Chemistry. 4: 3931-7. PMID 17047872 DOI: 10.1039/B611653A |
0.363 |
|
| 2006 |
Rungrotmongkol T, Mulholland AJ, Hannongbua S. Active site dynamics and combined quantum mechanics/molecular mechanics (QM/MM) modelling of a HIV-1 reverse transcriptase/DNA/dTTP complex. Journal of Molecular Graphics & Modelling. 26: 1-13. PMID 17046299 DOI: 10.1016/J.JMGM.2006.09.004 |
0.334 |
|
| 2006 |
Claeyssens F, Harvey JN, Manby FR, Mata RA, Mulholland AJ, Ranaghan KE, Schütz M, Thiel S, Thiel W, Werner HJ. High-accuracy computation of reaction barriers in enzymes. Angewandte Chemie (International Ed. in English). 45: 6856-9. PMID 16991165 DOI: 10.1002/Anie.200602711 |
0.397 |
|
| 2006 |
Sutcliffe MJ, Masgrau L, Roujeinikova A, Johannissen LO, Hothi P, Basran J, Ranaghan KE, Mulholland AJ, Leys D, Scrutton NS. Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: flavoprotein and quinoprotein systems. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 1375-86. PMID 16873125 DOI: 10.1098/rstb.2006.1878 |
0.346 |
|
| 2006 |
Mulholland AJ. Modelling enzyme reaction mechanisms, specificity and catalysis. Drug Discovery Today. 10: 1393-402. PMID 16253878 DOI: 10.1016/S1359-6446(05)03611-1 |
0.353 |
|
| 2005 |
Claeyssens F, Ranaghan KE, Manby FR, Harvey JN, Mulholland AJ. Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization. Chemical Communications (Cambridge, England). 5068-70. PMID 16220173 DOI: 10.1039/B508181E |
0.323 |
|
| 2005 |
Hermann JC, Hensen C, Ridder L, Mulholland AJ, Höltje HD. Mechanisms of antibiotic resistance: QM/MM modeling of the acylation reaction of a class A beta-lactamase with benzylpenicillin. Journal of the American Chemical Society. 127: 4454-65. PMID 15783228 DOI: 10.1021/ja044210d |
0.35 |
|
| 2005 |
Szefczyk B, Mulholland AJ, Ranaghan KE, Sokalski WA. Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field. Journal of the American Chemical Society. 126: 16148-59. PMID 15584751 DOI: 10.1021/JA049376T |
0.346 |
|
| 2004 |
Ranaghan KE, Mulholland AJ. Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase. Chemical Communications (Cambridge, England). 1238-9. PMID 15136856 DOI: 10.1039/B402388A |
0.34 |
|
| 2004 |
Ranaghan KE, Ridder L, Szefczyk B, Sokalski WA, Hermann JC, Mulholland AJ. Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction. Organic & Biomolecular Chemistry. 2: 968-80. PMID 15034619 DOI: 10.1039/b313759g |
0.369 |
|
| 2004 |
RUNGROTMONGKOL T, HANNONGBUA S, MULHOLLAND A. MECHANISTIC STUDY OF HIV-1 REVERSE TRANSCRIPTASE AT THE ACTIVE SITE BASED ON QM/MM METHOD Journal of Theoretical and Computational Chemistry. 3: 491-500. DOI: 10.1142/S0219633604001252 |
0.396 |
|
| 2003 |
Ridder L, Mulholland AJ. Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: from structure to activity. Current Topics in Medicinal Chemistry. 3: 1241-56. PMID 12769703 DOI: 10.2174/1568026033452005 |
0.378 |
|
| 2003 |
Ridder L, Harvey JN, Rietjens IMCM, Vervoort J, Mulholland AJ. Ab Initio QM/MM Modeling of the Hydroxylation Step inp-Hydroxybenzoate Hydroxylase The Journal of Physical Chemistry B. 107: 2118-2126. DOI: 10.1021/Jp026213N |
0.308 |
|
| 2002 |
Ridder L, Rietjens IM, Vervoort J, Mulholland AJ. Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide. Journal of the American Chemical Society. 124: 9926-36. PMID 12175255 DOI: 10.1021/JA0256360 |
0.389 |
|
| 2000 |
Ridder L, Mulholland AJ, Rietjens IM, Vervoort J. Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase. Journal of Molecular Graphics & Modelling. 17: 163-75, 214. PMID 10736773 DOI: 10.1016/S1093-3263(99)00027-3 |
0.307 |
|
| 2000 |
Mulholland AJ, Lyne PD, Karplus M. Ab Initio QM/MM Study of the Citrate Synthase Mechanism. A Low-Barrier Hydrogen Bond Is not Involved Journal of the American Chemical Society. 122: 534-535. DOI: 10.1021/Ja992874V |
0.388 |
|
| 1999 |
Mulholland AJ, Richards WG. Modeling the citrate synthase reaction: QM/MM and small model calculations Acs Symposium Series. 721: 448-461. |
0.472 |
|
| 1997 |
Mulholland AJ, Richards WG. Acetyl-CoA enolization in citrate synthase: A quantum mechanical/molecular mechanical (QM/MM) study Proteins: Structure, Function and Genetics. 27: 9-25. PMID 9037708 DOI: 10.1002/(SICI)1097-0134(199701)27:1<9::AID-PROT3>3.0.CO;2-D |
0.565 |
|
| 1996 |
Mulholland AJ, Karplus M. Simulations of enzymic reactions. Biochemical Society Transactions. 24: 247-54. PMID 8674677 DOI: 10.1042/Bst0240247 |
0.5 |
|
| 1995 |
Lyne PD, Mulholland AJ, Richards WG. Insights into Chorismate Mutase Catalysis from a Combined QM/MM Simulation of the Enzyme Reaction Journal of the American Chemical Society. 117: 11345-11350. DOI: 10.1021/JA00150A037 |
0.354 |
|
| 1995 |
Elcock AH, Lyne PD, Mulholland AJ, Nandra A, Richards WG. Combined quantum and molecular mechanical study of DNA cross-linking by nitrous acid Journal of the American Chemical Society. 117: 4706-4707. DOI: 10.1021/Ja00121A029 |
0.434 |
|
| 1994 |
Mulholland AJ, Richards WG. A comparison of semiempirical and ab initio transition states for HF elimination in unimolecular decompositions International Journal of Quantum Chemistry. 51: 161-172. DOI: 10.1002/Qua.560510306 |
0.45 |
|
| 1993 |
Mulholland AJ, Grant GH, Richards WG. Computer modelling of enzyme catalysed reaction mechanisms Protein Engineering. 6: 133-147. PMID 8475041 DOI: 10.1093/protein/6.2.133 |
0.552 |
|
| 1991 |
Balint-Kurti GG, Dixon RN, Clay Marston C, Mulholland AJ. The calculation of product quantum state distributions and partial cross-sections in time-dependent molecular collision and photodissociation theory Computer Physics Communications. 63: 126-134. DOI: 10.1016/0010-4655(91)90244-F |
0.525 |
|
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