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1

Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems

Kamerlin, Shina C.L., Vicatos, Spyridon, Dryga, Anatoly, Warshel, Arieh

Journal:

Annual Review of Physical Chemistry

Year:

2011

Language:

english

File:

PDF, 977 KB

english, 2011

2

Why nature really chose phosphate

Kamerlin, Shina C. L., Sharma, Pankaz K., Prasad, Ram B., Warshel, Arieh

Journal:

Quarterly Reviews of Biophysics

Year:

2013

Language:

english

File:

PDF, 3.76 MB

english, 2013

3

Collapse Dynamics of Core–Shell Nanogels

Kamerlin, Natasha, Elvingson, Christer

Journal:

Year:

2016

Language:

english

File:

PDF, 7.20 MB

english, 2016

4

At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Shina C. L. Kamerlin, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.24 MB

english, 2010

5

The empirical valence bond model: theory and applications

Shina C. L. Kamerlin, Arieh Warshel

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2011

Language:

english

File:

PDF, 229 KB

english, 2011

6

Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks

Plotnikov, Nikolay V., Kamerlin, Shina C. L., Warshel, Arieh

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 1.21 MB

english, 2011

7

The Conformation of a Catalytic Loop Is Central to GTPase Activity on the Ribosome

Åqvist, Johan, Kamerlin, Shina C. L.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.15 MB

english, 2015

8

Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations

Bauer, Paul, Barrozo, Alexandre, Purg, Miha, Amrein, Beat Anton, Esguerra, Mauricio, Wilson, Philippe Barrie, Major, Dan Thomas, Åqvist, Johan, Kamerlin, Shina Caroline Lynn

Journal:

Year:

2018

Language:

english

File:

PDF, 1.34 MB

english, 2018

9

Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase

Maršavelski, Aleksandra, Petrović, Dušan, Bauer, Paul, Vianello, Robert, Kamerlin, Shina Caroline Lynn

Journal:

Year:

2018

Language:

english

File:

PDF, 1.60 MB

english, 2018

10

Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε

Parkash, Vimal, Kulkarni, Yashraj, ter Beek, Josy, Shcherbakova, Polina V., Kamerlin, Shina Caroline Lynn, Johansson, Erik

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 2.99 MB

english, 2019

11

Managing COVID-19 spread with voluntary public-health measures: Sweden as a case study for pandemic control

Kamerlin, Shina C L, Kasson, Peter M

Journal:

Clinical Infectious Diseases

Year:

2020

File:

PDF, 536 KB

2020

12

Associative Versus Dissociative Mechanisms of Phosphate Monoester Hydrolysis: On the Interpretation of Activation Entropies

Shina C. L. Kamerlin, Jan Florián, Arieh Warshel

Journal:

Year:

2008

Language:

english

File:

PDF, 335 KB

english, 2008

13

Are Mixed Explicit/Implicit Solvation Models Reliable for Studying Phosphate Hydrolysis? A Comparative Study of Continuum, Explicit and Mixed Solvation Models

Shina C. L. Kamerlin, Maciej Haranczyk, Arieh Warshel

Journal:

Year:

2009

Language:

english

File:

PDF, 365 KB

english, 2009

14

Characterisation by 1H NMR spectroscopy of enzymically derived oligosaccharides from alkali-extractable wheat-flour arabinoxylan

Harry Gruppen, Rainer A. Hoffmaann, Felix J.M. Kormelink, Alphons G.J. Voragen, Johannis P. Kamerlin, Johannes F.G. Vliegenthart

Journal:

Carbohydrate Research

Year:

1992

Language:

english

File:

PDF, 1.05 MB

english, 1992

15

An analysis of all the relevant facts and arguments indicates that enzyme catalysis does not involve large contributions from nuclear tunneling

Shina C. L. Kamerlin, Arieh Warshel

Journal:

Journal of Physical Organic Chemistry

Year:

2010

Language:

english

File:

PDF, 330 KB

english, 2010

16

Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase: A comparison to analogous phosphatases

Jinghui Luo, Bert van Loo, S. C. L. Kamerlin

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.35 MB

english, 2012

17

Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues

Shina Caroline Lynn Kamerlin, Janez Mavri, A. Warshel

Journal:

Year:

2010

Language:

english

File:

PDF, 612 KB

english, 2010

18

Catalytic promiscuity in Pseudomonas aeruginosa arylsulfatase as an example of chemistry-driven protein evolution

Jinghui Luo, Bert van Loo, Shina C.L. Kamerlin

Journal:

Year:

2012

Language:

english

File:

PDF, 1.06 MB

english, 2012

19

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

Adamczyk, A. J., Cao, J., Kamerlin, S. C. L., Warshel, A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 760 KB

english, 2011

20

A targeted molecular dynamics study of WPD loop movement in PTP1B

Shina Caroline Lynn Kamerlin, Robert Rucker, Stefan Boresch

Journal:

Biochemical and Biophysical Research Communications

Year:

2006

Language:

english

File:

PDF, 615 KB

english, 2006

21

A molecular dynamics study of WPD-loop flexibility in PTP1B

Shina Caroline Lynn Kamerlin, Robert Rucker, Stefan Boresch

Journal:

Biochemical and Biophysical Research Communications

Year:

2007

Language:

english

File:

PDF, 631 KB

english, 2007

22

On the Interpretation of the Observed Linear Free Energy Relationship in Phosphate Hydrolysis: A Thorough Computational Study of Phosphate Diester Hydrolysis in Solution †

Rosta, Edina, Kamerlin, Shina C. L., Warshel, Arieh

Journal:

Year:

2008

Language:

english

File:

PDF, 1.35 MB

english, 2008

23

The effect of leaving group on mechanistic preference in phosphate monoester hydrolysis

Kamerlin, Shina C. L., Wilkie, John

Journal:

Organic & Biomolecular Chemistry

Year:

2011

Language:

english

File:

PDF, 1.02 MB

english, 2011

24

Cellular Polyamines Promote Amyloid-Beta (Aβ) Peptide Fibrillation and Modulate the Aggregation Pathways

Luo, Jinghui, Yu, Chien-Hung, Yu, Huixin, Borstnar, Rok, Kamerlin, Shina C. L., Gräslund, Astrid, Abrahams, Jan Pieter, Wärmländer, Sebastian K. T. S.

Journal:

ACS Chemical Neuroscience

Year:

2013

Language:

english

File:

PDF, 3.88 MB

english, 2013

25

The role of metal ions in phosphate ester hydrolysis

Kamerlin, Shina C. L., Wilkie, John

Journal:

Organic & Biomolecular Chemistry

Year:

2007

Language:

english

File:

PDF, 449 KB

english, 2007

26

Modeling catalytic promiscuity in the alkaline phosphatase superfamily

Duarte, Fernanda, Amrein, Beat Anton, Kamerlin, Shina Caroline Lynn

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 3.02 MB

english, 2013

27

Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting

B. Ram Prasad, S. C. L. Kamerlin, Jan Florián…

Journal:

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

Year:

2012

Language:

english

File:

PDF, 449 KB

english, 2012

28

Brownian dynamics of a compressed polymer brush model. Off-equilibrium response as a function of surface coverage and compression rate

Carlsson, T., Kamerlin, N., Arteca, G. A., Elvingson, C.

Journal:

Physical Chemistry Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.16 MB

english, 2011

29

The Alkaline Hydrolysis of Sulfonate Esters: Challenges in Interpreting Experimental and Theoretical Data

Duarte, Fernanda, Geng, Ting, Marloie, Gaël, Al Hussain, Adel O., Williams, Nicholas H., Kamerlin, Shina Caroline Lynn

Journal:

Journal of Organic Chemistry

Year:

2014

Language:

english

File:

PDF, 3.04 MB

english, 2014

30

Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of p K a , Redox Reactions and Solvation Free Energies †

Kamerlin, Shina C. L., Haranczyk, Maciej, Warshel, Arieh

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 1.65 MB

english, 2009

31

Concerted or Stepwise: How Much Do Free-Energy Landscapes Tell Us about the Mechanisms of Elimination Reactions?

Duarte, Fernanda, Gronert, Scott, Kamerlin, Shina Caroline Lynn

Journal:

Journal of Organic Chemistry

Year:

2014

Language:

english

File:

PDF, 2.14 MB

english, 2014

32

Enzyme Millisecond Conformational Dynamics Do Not Catalyze the Chemical Step

Pisliakov, Andrei V., Cao, Jie, Kamerlin, Shina C.L., Warshel, Arieh

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 30 KB

english, 2010

33

Rationalizing the Catalytic Activity of an Unusual Oxidoreductase (FucO)

Duarte, Fernanda, Caroline, Shina, Kamerlin, Lynn

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 35 KB

english, 2013

34

Cellular Polyamines Promote Amyloid-Beta Peptide Fibrillation and Modulate the Aggregation Pathways

Luo, Jinghui, Yu, Chien-Hung, Yu, Huixin, Borstnar, Rok, Kamerlin, Shina C.L., Gräslund, Astrid, Pieter Abrahams, Jan, Wärmländer, Sebastian K.T.S.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 70 KB

english, 2013

35

On the Energetics of ATP Hydrolysis in Solution

Kamerlin, Shina C. L., Warshel, Arieh

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 523 KB

english, 2009

36

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

Duarte, Fernanda, Bauer, Paul, Barrozo, Alexandre, Amrein, Beat Anton, Purg, Miha, Åqvist, Johan, Kamerlin, Shina Caroline Lynn

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 2.57 MB

english, 2014

37

Editorial overview: Mechanisms: Chemical and computational probes of biological mechanism

O’Donoghue, AnnMarie C, Kamerlin, Shina C.L.

Journal:

Current Opinion in Chemical Biology

Year:

2014

Language:

english

File:

PDF, 134 KB

english, 2014

38

A Computational Study of the Hydrolysis of dGTP Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases

Kamerlin, Shina C. L., McKenna, Charles E., Goodman, Myron F., Warshel, A.

Journal:

Year:

2009

Language:

english

File:

PDF, 1.49 MB

english, 2009

39

On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems with the Gas-Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models

Kamerlin, Shina C. L., Chu, Zhen T., Warshel, A.

Journal:

Journal of Organic Chemistry

Year:

2010

Language:

english

File:

PDF, 1.69 MB

english, 2010

40

Multiscale modeling of biological functions

Kamerlin, Shina Caroline Lynn, Warshel, Arieh

Journal:

Physical Chemistry Chemical Physics

Year:

2011

Language:

english

File:

PDF, 2.02 MB

english, 2011

41

Challenges in computational studies of enzyme structure, function and dynamics

Carvalho, Alexandra T.P., Barrozo, Alexandre, Doron, Dvir, Kilshtain, Alexandra Vardi, Major, Dan Thomas, Kamerlin, Shina Caroline Lynn

Journal:

Journal of Molecular Graphics and Modelling

Year:

2014

Language:

english

File:

PDF, 16.81 MB

english, 2014

42

Dineopentyl Phosphate Hydrolysis: Evidence for Stepwise Water Attack

Kamerlin, Shina C. L., Williams, Nicholas H., Warshel, Arieh

Journal:

Journal of Organic Chemistry

Year:

2008

Language:

english

File:

PDF, 1.31 MB

english, 2008

43

Empirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamine

Repič, Matej, Vianello, Robert, Purg, Miha, Duarte, Fernanda, Bauer, Paul, Kamerlin, Shina C. L., Mavri, Janez

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.30 MB

english, 2014

44

On Unjustifiably Misrepresenting the EVB Approach While Simultaneously Adopting It

Kamerlin, Shina C. L., Cao, Jie, Rosta, Edina, Warshel, Arieh

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 2.50 MB

english, 2009

45

Computational Study of the p K a Values of Potential Catalytic Residues in the Active Site of Monoamine Oxidase B

Borštnar, Rok, Repič, Matej, Kamerlin, Shina Caroline Lynn, Vianello, Robert, Mavri, Janez

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 3.48 MB

english, 2012

46

Base-Catalyzed Dehydration of 3-Substituted Benzene cis -1,2-Dihydrodiols: Stabilization of a Cyclohexadienide Anion Intermediate by Negative Aromatic Hyperconjugation

Kudavalli, Jaya Satyanarayana, Rao, S. Nagaraja, Bean, David E., Sharma, Narain D., Boyd, Derek R., Fowler, Patrick W., Gronert, Scott, Kamerlin, Shina Caroline Lynn, Keeffe, James R., More O’Ferrall,

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 1.34 MB

english, 2012

47

Correction to A Computational Study of the Hydrolysis of dGTP Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases

Kamerlin, Shina C. L., McKenna, Charles E., Goodman, Myron F., Warshel, A.

Journal:

Year:

2009

Language:

english

File:

PDF, 558 KB

english, 2009

48

Theoretical Comparison of p -Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer

Kamerlin, Shina Caroline Lynn

Journal:

Journal of Organic Chemistry

Year:

2011

Language:

english

File:

PDF, 1.19 MB

english, 2011

49

Energetics of activation of GTP hydrolysis on the ribosome

Wallin, Göran, Kamerlin, Shina C. L., Åqvist, Johan

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 2.38 MB

english, 2013

50

How valence bond theory can help you understand your (bio)chemical reaction

Shurki, Avital, Derat, Etienne, Barrozo, Alexandre, Kamerlin, Shina Caroline Lynn

Journal:

Chemical Society Reviews

Year:

2015

Language:

english

File:

PDF, 3.21 MB

english, 2015

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