Adrian J. Mulholland: search on Z-Library

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1

Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods

Ranaghan, Kara E., Mulholland, Adrian J.

Journal:

International Reviews in Physical Chemistry

Year:

2010

Language:

english

File:

PDF, 2.65 MB

english, 2010

2

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

van der Kamp, Marc W., Mulholland, Adrian J.

Journal:

Year:

2013

Language:

english

File:

PDF, 4.75 MB

english, 2013

3

QM/MM Study on Cleavage Mechanism Catalyzed by Zika Virus NS2B/NS3 Serine Protease

Nutho, Bodee, Mulholland, Adrian, Rungrotmongkol, Thanyada

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 44 KB

english, 2019

4

Multiscale methods in drug design bridge chemical and biological complexity in the search for cures

Amaro, Rommie E., Mulholland, Adrian J.

Journal:

Nature Reviews Chemistry

Year:

2018

Language:

english

File:

PDF, 4.29 MB

english, 2018

5

Computational enzymology: insight into biological catalysts from modelling

van der Kamp, Marc W., Mulholland, Adrian J.

Journal:

Natural Product Reports

Year:

2008

Language:

english

File:

PDF, 2.15 MB

english, 2008

6

Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase

Lawan, Narin, Ranaghan, Kara E., Manby, Frederick R., Mulholland, Adrian J.

Journal:

Chemical Physics Letters

Year:

2014

Language:

english

File:

PDF, 954 KB

english, 2014

7

An efficient method for the calculation of quantum mechanics/molecular mechanics free energies

Woods, Christopher J., Manby, Frederick R., Mulholland, Adrian J.

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 765 KB

english, 2008

8

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

Raza, Saad, Ranaghan, Kara E., van der Kamp, Marc W., Woods, Christopher J., Mulholland, Adrian J., Azam, Syed Sikander

Journal:

Journal of Computer-Aided Molecular Design

Year:

2019

Language:

english

File:

PDF, 3.39 MB

english, 2019

9

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

Nutho, Bodee, Mulholland, Adrian J., Rungrotmongkol, Thanyada

Journal:

Journal of Physical Chemistry B

Year:

2019

Language:

english

File:

PDF, 4.73 MB

english, 2019

10

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

Gerrard, Will, Bratholm, Lars A., Packer, Martin J., Mulholland, Adrian J., Glowacki, David R., Butts, Craig P.

Journal:

Chemical Science

Year:

2020

File:

PDF, 925 KB

2020

11

Computational enzymology

Lonsdale, Richard, Ranaghan, Kara E., Mulholland, Adrian J.

Journal:

Chemical Communications

Year:

2010

Language:

english

File:

PDF, 1.80 MB

english, 2010

12

Active-site dynamics of ASADH—A bacterial biosynthetic enzyme

Andrea T. Hadfield, Adrian J. Mulholland

Journal:

International Journal of Quantum Chemistry

Year:

1999

Language:

english

File:

PDF, 472 KB

english, 1999

13

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

Mlýnský, Vojtěch, Banáš, Pavel, Šponer, Jiří, van der Kamp, Marc W., Mulholland, Adrian J., Otyepka, Michal

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 6.03 MB

english, 2014

14

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

Lonsdale, Richard, Houghton, Kerensa T., Żurek, Jolanta, Bathelt, Christine M., Foloppe, Nicolas, de Groot, Marcel J., Harvey, Jeremy N., Mulholland, Adrian J.

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 14.17 MB

english, 2013

15

QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase

Jeremy N. Harvey, Christine M. Bathelt, Adrian J. Mulholland

Journal:

Journal of Computational Chemistry

Year:

2006

Language:

english

File:

PDF, 362 KB

english, 2006

16

Taking Ockham's razor to enzyme dynamics and catalysis

Glowacki, David R., Harvey, Jeremy N., Mulholland, Adrian J.

Journal:

Nature Chemistry

Year:

2012

Language:

english

File:

PDF, 1.19 MB

english, 2012

17

Protein dynamics and enzyme catalysis: Insights from simulations

John D. McGeagh, Kara E. Ranaghan, Adrian J. Mulholland

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2011

Language:

english

File:

PDF, 1.28 MB

english, 2011

18

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

Lonsdale, Richard, Harvey, Jeremy N., Mulholland, Adrian J.

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 516 KB

english, 2012

19

Insights into enzyme catalysis from QM/MM modelling: transition state stabilization in chorismate mutase

RANAGHAN, KARA E., RIDDER, LARS, SZEFCZYK, BORYS, SOKALSKI, W. ANDRZEJ, HERMANN, JOHANNES C., MULHOLLAND, ADRIAN J.

Journal:

Molecular Physics

Year:

2003

Language:

english

File:

PDF, 2.04 MB

english, 2003

20

QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate

Bowman, Anna L., Grant, Ian M., Mulholland, Adrian J.

Journal:

Chemical Communications

Year:

2008

Language:

english

File:

PDF, 381 KB

english, 2008

21

A projector embedding approach for multiscale coupled-cluster calculations applied to citrate synthase.

Bennie, Simon Jonathan, van der Kamp, Marc W., Pennifold, Robert C.R., Stella, Martina, Manby, Frederick R., Mulholland, Adrian J.

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 3.09 MB

english, 2016

22

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

Lence, Emilio, van der Kamp, Marc W., González-Bello, Concepción, Mulholland, Adrian J.

Journal:

Organic & Biomolecular Chemistry

Year:

2018

Language:

english

File:

PDF, 3.96 MB

english, 2018

23

Comment on “A stationary-wave model of enzyme catalysis” by Carlo Canepa

Richard Lonsdale, Jeremy N. Harvey, Frederick R. Manby, Adrian J. Mulholland

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 46 KB

english, 2011

24

Enzyme dynamics and catalysis in the mechanism of DNA polymerase

Adrian J. Mulholland, Adrian E. Roitberg, Iñaki Tuñón

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2012

Language:

english

File:

PDF, 187 KB

english, 2012

25

Conformational Change and Ligand Binding in the Aristolochene Synthase Catalytic Cycle

van der Kamp, Marc W., Sirirak, Jitnapa, Żurek, Jolanta, Allemann, Rudolf K., Mulholland, Adrian J.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.99 MB

english, 2013

26

Identification of Glu166 as the General Base in the Acylation Reaction of Class A β-Lactamases through QM/MM Modeling

Hermann, Johannes C., Ridder, Lars, Mulholland, Adrian J., Höltje, Hans-Dieter

Journal:

Journal of the American Chemical Society

Year:

2003

Language:

english

File:

PDF, 105 KB

english, 2003

27

Computational enzymology: modelling the mechanisms of biological catalysts: Figure 1

Mulholland, Adrian J.

Journal:

Biochemical Society Transactions

Year:

2008

Language:

english

File:

PDF, 254 KB

english, 2008

28

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

Zhang, Xinglong, Bennie, Simon J., van der Kamp, Marc W., Glowacki, David R., Manby, Frederick R., Mulholland, Adrian J.

Journal:

Royal Society Open Science

Year:

2018

Language:

english

File:

PDF, 736 KB

english, 2018

29

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions

Wells, Stephen A., van der Kamp, Marc W., McGeagh, John D., Mulholland, Adrian J., Soares, Claudio M

Journal:

Year:

2015

Language:

english

File:

PDF, 4.29 MB

english, 2015

30

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

Punkvang, Auradee, Kamsri, Pharit, Mulholland, Adrian, Spencer, James, Hannongbua, Supa, Pungpo, Pornpan

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 1.22 MB

english, 2019

31

An efficient computational assay for β-lactam antibiotic breakdown by class A β-lactamases

Hirvonen, Viivi, Hammond, Katharine, Chudyk, Ewa I, Limb, Michael, Spencer, James, Mulholland, Adrian J., van der Kamp, Marc W.

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 1.13 MB

english, 2019

32

Identification of productive inhibitor binding orientation in fatty acid amide hydrolase (FAAH) by QM/MM mechanistic modelling

Lodola, Alessio, Mor, Marco, Rivara, Silvia, Christov, Christo, Tarzia, Giorgio, Piomelli, Daniele, Mulholland, Adrian J.

Journal:

Chemical Communications

Year:

2008

Language:

english

File:

PDF, 261 KB

english, 2008

33

A qualitative phenomenological analysis of the subjective experience and understanding of the at risk mental state

Brew, Benjamin, Shannon, Ciaran, Storey, Lesley, Boyd, Adrian, Mulholland, Ciaran

Journal:

International Journal of Qualitative Studies on Health and Well-Being

Year:

2017

Language:

english

File:

PDF, 1.28 MB

english, 2017

34

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

Ge, Yushu, van der Kamp, Marc, Malaisree, Maturos, Liu, Dan, Liu, Yi, Mulholland, Adrian J.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2017

Language:

english

File:

PDF, 1.78 MB

english, 2017

35

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

Voice, Angus, Tresadern, Gary, Van Vlijmen, Herman, Mulholland, Adrian J.

Journal:

Journal of Chemical Information and Modeling

Year:

2019

File:

PDF, 7.88 MB

2019

36

Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions

Claeyssens, Frederik, Ranaghan, Kara E., Lawan, Narin, Macrae, Stephen J., Manby, Frederick R., Harvey, Jeremy N., Mulholland, Adrian J.

Journal:

Organic & Biomolecular Chemistry

Year:

2011

Language:

english

File:

PDF, 659 KB

english, 2011

37

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

Chudyk, Ewa I., Dyguda-Kazimierowicz, Edyta, Langner, Karol M., Sokalski, W. Andrzej, Lodola, Alessio, Mor, Marco, Sirirak, Jitnapa, Mulholland, Adrian J.

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 1.59 MB

english, 2013

38

Combined Quantum and Molecular Mechanical Study of DNA Crosslinking by Nitrous Acid

Elcock, Adrian H., Lyne, Paul D., Mulholland, Adrian J., Nandra, Ankush, Richards, W. Graham

Journal:

Journal of the American Chemical Society

Year:

1995

Language:

english

File:

PDF, 703 KB

english, 1995

39

Modeling Enzyme Reaction Intermediates and Transition States: Citrate Synthase

Mulholland, Adrian J., Richards, W. Graham

Journal:

Journal of Physical Chemistry B

Year:

1998

Language:

english

File:

PDF, 353 KB

english, 1998

40

QM/MM Free-Energy Simulations of Reaction in Serratia marcescens Chitinase B Reveal the Protonation State of Asp142 and the Critical Role of Tyr214

Jitonnom, Jitrayut, Limb, Michael A. L., Mulholland, Adrian J.

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 661 KB

english, 2014

41

Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics/Molecular Mechanics Liquid Water Simulations

Shaw, Katherine E., Woods, Christopher J., Mulholland, Adrian J.

Journal:

The Journal of Physical Chemistry Letters

Year:

2010

Language:

english

File:

PDF, 1.65 MB

english, 2010

42

High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase

van der Kamp, Marc W., Perruccio, Francesca, Mulholland, Adrian J.

Journal:

Chemical Communications

Year:

2008

Language:

english

File:

PDF, 601 KB

english, 2008

43

Large-Scale Density Functional Theory Transition State Searching in Enzymes

Lever, Greg, Cole, Daniel J., Lonsdale, Richard, Ranaghan, Kara E., Wales, David J., Mulholland, Adrian J., Skylaris, Chris-Kriton, Payne, Mike C.

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 1.90 MB

english, 2014

44

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

Woods, Christopher J., Malaisree, Maturos, Long, Ben, McIntosh-Smith, Simon, Mulholland, Adrian J.

Journal:

Scientific Reports

Year:

2013

Language:

english

File:

PDF, 920 KB

english, 2013

45

Experiment and simulation reveal how mutations in functional plasticity regions guide plant monoterpene synthase product outcome

Leferink, Nicole G.H., Ranaghan, Kara, Karrupiah, Vijaykumar, Currin, Andrew, van der Kamp, Marc, Mulholland, Adrian J., Scrutton, Nigel S.

Journal:

Year:

2018

Language:

english

File:

PDF, 2.43 MB

english, 2018

46

Dynamical origins of heat capacity changes in enzyme-catalysed reactions

van der Kamp, Marc W., Prentice, Erica J., Kraakman, Kirsty L., Connolly, Michael, Mulholland, Adrian J., Arcus, Vickery L.

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 1.14 MB

english, 2018

47

Differential Transition-State Stabilization in Enzyme Catalysis: Quantum Chemical Analysis of Interactions in the Chorismate Mutase Reaction and Prediction of the Optimal Catalytic Field

Szefczyk, Borys, Mulholland, Adrian J., Ranaghan, Kara E., Sokalski, W. Andrzej

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 329 KB

english, 2004

48

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

Rydberg, Patrik, Lonsdale, Richard, Harvey, Jeremy N., Mulholland, Adrian J., Olsen, Lars

Journal:

Journal of Molecular Graphics and Modelling

Year:

2014

Language:

english

File:

PDF, 446 KB

english, 2014

49

Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization

Claeyssens, Frederik, Ranaghan, Kara E., Manby, Frederick R., Harvey, Jeremy N., Mulholland, Adrian J.

Journal:

Chemical Communications

Year:

2005

Language:

english

File:

PDF, 308 KB

english, 2005

50

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

van der Kamp, Marc W., Chaudret, Robin, Mulholland, Adrian J.

Journal:

Year:

2013

Language:

english

File:

PDF, 540 KB

english, 2013

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