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1

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

2

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

3

From artificial neural networks to spiking neuron populations and back again

Marc de Kamps, Frank van der Velde

Journal:

Neural Networks

Year:

2001

Language:

english

File:

PDF, 424 KB

english, 2001

4

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

5

Quantum Mechanics/Molecular Mechanics Simulations Identify the Ring-Opening Mechanism of Creatininase

Jitonnom, Jitrayut, Mujika, Jon I., van der Kamp, Marc W., Mulholland, Adrian J.

Journal:

Year:

2017

Language:

english

File:

PDF, 6.60 MB

english, 2017

6

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

7

Mitochondrial import, health and mtDNA copy number variability using type II and type V CRISPR effectors

AntÃ³n, ZuriÃ±e, Mullally, Grace, Ford, Holly, van der Kamp, Marc W., Szczelkun, Mark D., Lane, Jon D.

Journal:

Journal of Cell Science

Year:

2020

File:

PDF, 19.81 MB

2020

8

“Lethal Synthesis” of Fluorocitrate by Citrate Synthase Explained through QM/MM Modeling

Dr. Marc W. van der Kamp, John D. McGeagh, Prof. Adrian J. Mulholland

Journal:

Angewandte Chemie

Year:

2011

Language:

english

File:

PDF, 474 KB

english, 2011

9

“Lethal Synthesis” of Fluorocitrate by Citrate Synthase Explained through QM/MM Modeling

Dr. Marc W. van der Kamp, John D. McGeagh, Prof. Adrian J. Mulholland

Journal:

Angewandte Chemie International Edition

Year:

2011

Language:

english

File:

PDF, 457 KB

english, 2011

10

The state of MIIND

Marc de Kamps, Volker Baier, Johannes Drever, Melanie Dietz, Lorenz Mösenlechner, Frank van der Velde

Journal:

Neural Networks

Year:

2008

Language:

english

File:

PDF, 6.08 MB

english, 2008

11

Learning of control in a neural architecture of grounded language processing

Frank van der Velde, Marc de Kamps

Journal:

Cognitive Systems Research

Year:

2010

Language:

english

File:

PDF, 295 KB

english, 2010

12

Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase

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

Journal:

Journal of Molecular Graphics and Modelling

Year:

2007

Language:

english

File:

PDF, 378 KB

english, 2007

13

Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl-CoA enolization in citrate synthase

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 361 KB

english, 2007

14

Affinity of Avr2 for tomato cysteine protease Rcr3 correlates with the Avr2-triggered Cf-2-mediated hypersensitive response

JOHN W. VAN'T KLOOSTER, MARC W. VAN DER KAMP, JACQUES VERVOORT, JULES BEEKWILDER, SJEF BOEREN, MATTHIEU H. A. J. JOOSTEN, BART P. H. J. THOMMA, PIERRE J. G. M. DE WIT

Journal:

Molecular Plant Pathology

Year:

2011

Language:

english

File:

PDF, 468 KB

english, 2011

15

Synchrony in the Eye of the Beholder: An Analysis of the Role of Neural Synchronization in Cognitive Processes

Frank van der Velde, Marc de Kamps

Journal:

Year:

2002

Language:

english

File:

PDF, 159 KB

english, 2002

16

Diverse Effects on the Native β-Sheet of the Human Prion Protein Due to Disease-Associated Mutations

Chen, Wei, van der Kamp, Marc W., Daggett, Valerie

Journal:

Year:

2010

Language:

english

File:

PDF, 4.56 MB

english, 2010

17

CLAM: Closed-loop attention model for visual search

Frank van der Velde, Marc de Kamps, Gwendid T. van der Voort van der Kleij

Journal:

Year:

2004

Language:

english

File:

PDF, 195 KB

english, 2004

18

Increasing number of objects impairs binding in visual working memory

Gwendid T. van der Voort van der Kleij, Marc de Kamps, Frank van der Velde

Journal:

Year:

2004

Language:

english

File:

PDF, 221 KB

english, 2004

19

Dynameomics: A Comprehensive Database of Protein Dynamics

Marc W. van der Kamp, R. Dustin Schaeffer, Amanda L. Jonsson, Alexander D. Scouras, Andrew M. Simms, Rudesh D. Toofanny, Noah C. Benson, Peter C. Anderson, Eric D. Merkley, Steven Rysavy, Dennis Broml

Journal:

Year:

2010

Language:

english

File:

PDF, 2.07 MB

english, 2010

20

Using a recurrent network to bind form, color and position into a unified percept

Marc de Kamps, Frank van der Velde

Journal:

Year:

2001

Language:

english

File:

PDF, 160 KB

english, 2001

21

Implementation of multilayer perceptron networks by populations of spiking neurons using rate coding

Marc de Kamps, Frank van der Velde

Journal:

Year:

2002

Language:

english

File:

PDF, 78 KB

english, 2002

22

Dynamic aspects of delay activity

Marc de Kamps, Frank van der Velde

Journal:

Year:

2003

Language:

english

File:

PDF, 255 KB

english, 2003

23

A model of visual working memory in PFC

Frank van der Velde, Marc de Kamps

Journal:

Year:

2003

Language:

english

File:

PDF, 179 KB

english, 2003

24

Biomolecular simulation and modelling: status, progress and prospects

van der Kamp, Marc W., Shaw, Katherine E., Woods, Christopher J., Mulholland, Adrian J.

Journal:

Journal of The Royal Society Interface

Year:

2008

Language:

english

File:

PDF, 559 KB

english, 2008

25

Pathogenic Mutations in the Hydrophobic Core of the Human Prion Protein Can Promote Structural Instability and Misfolding

Marc W. van der Kamp, Valerie Daggett

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 2.50 MB

english, 2010

26

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

Fonseca, Fátima, Chudyk, Ewa I., van der Kamp, Marc W., Correia, António, Mulholland, Adrian J., Spencer, James

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 1.53 MB

english, 2012

27

Influence of pH on the Human Prion Protein: Insights into the Early Steps of Misfolding

van der Kamp, Marc W., Daggett, Valerie

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 1.33 MB

english, 2010

28

Prognostic value of markers of myocardial damage and inflammation in low to intermediate risk chest pain patients

Radha Bholasingh, Jan H. Cornel, Otto Kamp, Alphons Windhausen, Marc van der Zee, Jan van Straalen, Gerard T. Sanders, Robbert J. de Winter

Journal:

Journal of the American College of Cardiology

Year:

2002

Language:

english

File:

PDF, 72 KB

english, 2002

29

Germline Epigenetic Silencing of the Tumor Suppressor Gene PTPRJ in Early-Onset Familial Colorectal Cancer

Ramprasath Venkatachalam, Marjolijn J.L. Ligtenberg, Nicoline Hoogerbrugge, Hans K. Schackert, Heike Görgens, Marc-Manuel Hahn, Eveline J. Kamping, Lilian Vreede, Eveline Hoenselaar, Erica van der Loo

Journal:

Gastroenterology

Year:

2010

Language:

english

File:

PDF, 871 KB

english, 2010

30

Comparison of Different Quantum Mechanical/Molecular Mechanics Boundary Treatments in the Reaction of the Hepatitis C Virus NS3 Protease with the NS5A/5B Substrate

Rodríguez, Alejandro, Oliva, Carolina, González, Miguel, van der Kamp, Marc, Mulholland, Adrian J.

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 412 KB

english, 2007

31

Dynameomics: protein dynamics and unfolding across fold space

Jonsson, Amanda L., Schaeffer, R. Dustin, van der Kamp, Marc W., Daggett, Valerie

Journal:

BioMolecular Concepts

Year:

2010

Language:

english

File:

PDF, 436 KB

english, 2010

32

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

33

Structural and Dynamic Properties of the Human Prion Protein

Chen, Wei, van der Kamp, Marc W., Daggett, Valerie

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 3.35 MB

english, 2014

34

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

Daniels, Adam D., Campeotto, Ivan, van der Kamp, Marc W., Bolt, Amanda H., Trinh, Chi H., Phillips, Simon E. V., Pearson, Arwen R., Nelson, Adam, Mulholland, Adrian J., Berry, Alan

Journal:

ACS Chemical Biology

Year:

2014

Language:

english

File:

PDF, 2.70 MB

english, 2014

35

Lack of combinatorial productivity in language processing with simple recurrent networks

van der Velde, Frank, van der Voort van der Kleij, Gwendid T., de Kamps, Marc

Journal:

Connection Science

Year:

2004

Language:

english

File:

PDF, 202 KB

english, 2004

36

Testing High-Level QM/MM Methods for Modeling Enzyme Reactions: Acetyl-CoA Deprotonation in Citrate Synthase

van der Kamp, Marc W., Żurek, Jolanta, Manby, Frederick R., Harvey, Jeremy N., Mulholland, Adrian J.

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 2.00 MB

english, 2010

37

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

38

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

Chudyk, Ewa I., Limb, Michael A. L., Jones, Charlotte, Spencer, James, van der Kamp, Marc W., Mulholland, Adrian J.

Journal:

Chemical Communications

Year:

2014

Language:

english

File:

PDF, 2.09 MB

english, 2014

39

[IEEE 2011 IEEE International Conference on Development and Learning (ICDL) - Frankfurt am Main, Germany (2011.08.24-2011.08.27)] 2011 IEEE International Conference on Development and Learning (ICDL) - Development of a connection matrix for productive grounded cognition

van der Velde, Frank, de Kamps, Marc

Year:

2011

Language:

english

File:

PDF, 1011 KB

english, 2011

40

Compositional connectionist structures based on in situ grounded representations

van der Velde, Frank, de Kamps, Marc

Journal:

Connection Science

Year:

2011

Language:

english

File:

PDF, 315 KB

english, 2011

41

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

42

[IEEE 2008 IEEE International Joint Conference on Neural Networks (IJCNN 2008 - Hong Kong) - Hong Kong, China (2008.06.1-2008.06.8)] 2008 IEEE International Joint Conference on Neural Networks (IEEE World Congress on Computational Intelligence) - A neural architecture for grounded cognition: Representation, structure, dynamics and learning

van der Velde, Frank, de Kamps, Marc

Year:

2008

File:

PDF, 334 KB

2008

43

Neural blackboard architectures: the realization of compositionality and systematicity in neural networks

Kamps, Marc de, Velde, Frank van der

Journal:

Journal of Neural Engineering

Year:

2006

Language:

english

File:

PDF, 282 KB

english, 2006

44

From Knowing What to Knowing Where: Modeling Object-Based Attention with Feedback Disinhibition of Activation

van der Velde, Frank, de Kamps, Marc

Journal:

Journal of Cognitive Neuroscience

Year:

2001

Language:

english

File:

PDF, 7.30 MB

english, 2001

45

The necessity of connection structures in neural models of variable binding

van der Velde, Frank, de Kamps, Marc

Journal:

Cognitive Neurodynamics

Year:

2015

Language:

english

File:

PDF, 683 KB

english, 2015

46

On the Temperature Dependence of Enzyme-catalyzed Rates

Arcus, Vickery L., Prentice, Erica J., Hobbs, Joanne K., Mulholland, Adrian J., van der Kamp, Marc W., Pudney, Christopher Roland, Parker, Emily J., Schipper, Louis A.

Journal:

Year:

2016

Language:

english

File:

PDF, 786 KB

english, 2016

47

The catalytic mechanism of a natural Diels-Alderase revealed in molecular detail

Byrne, Matthew J., Lees, Nicholas R., Han, Li-Chen, van der Kamp, Marc W., Mulholland, Adrian J., Stach, James E. M., Willis, Christine L., Race, Paul R.

Journal:

Journal of the American Chemical Society

Year:

2016

Language:

english

File:

PDF, 1.17 MB

english, 2016

48

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

49

Neural blackboard architectures of combinatorial structures in cognition

van der Velde, Frank, de Kamps, Marc

Journal:

Behavioral and Brain Sciences

Year:

2006

Language:

english

File:

PDF, 1.20 MB

english, 2006

50

How Static Disorder Mimics Decoherence in Anisotropy Pump-Probe Experiments on Purple-Bacteria Light Harvesting Complexes

Stross, Clement, Van der Kamp, Marc W, Oliver, Thomas A. A., Harvey, Jeremy N, Linden, Noah, Manby, Frederick R.

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 1.41 MB

english, 2016

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