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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

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

4

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

5

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

6

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

7

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

8

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

9

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

10

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

11

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

12

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

13

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

14

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

15

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

16

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

17

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

18

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

19

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

20

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

21

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

22

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

23

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

24

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

25

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

26

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

27

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

28

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

29

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

30

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

31

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

32

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

33

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

34

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

35

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

36

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

37

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

38

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

39

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

40

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

41

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

42

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

43

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

44

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

45

Resolving Apparent Conflicts between Theoretical and Experimental Models of Phosphate Monoester Hydrolysis

Duarte, Fernanda, Åqvist, Johan, Williams, Nicholas H., Kamerlin, Shina C. L.

Journal:

Journal of the American Chemical Society

Year:

2015

Language:

english

File:

PDF, 2.48 MB

english, 2015

46

Recent advances in QM/MM free energy calculations using reference potentials

Duarte, Fernanda, Amrein, Beat A., Blaha-Nelson, David, Kamerlin, Shina C.L.

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Year:

2015

Language:

english

File:

PDF, 2.09 MB

english, 2015

47

Catalytic Stimulation by Restrained Active-Site Floppiness—The Case of High Density Lipoprotein-Bound Serum Paraoxonase-1

Ben-David, Moshe, Sussman, Joel L., Maxwell, Christopher I., Szeler, Klaudia, Kamerlin, Shina C.L., Tawfik, Dan S.

Journal:

Journal of Molecular Biology

Year:

2015

Language:

english

File:

PDF, 1.49 MB

english, 2015

48

Reply to Karplus: Conformational dynamics have no role in the chemical step

Kamerlin, Shina C. L., Warshel, Arieh

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 428 KB

english, 2010

49

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

Carvalho, Alexandra T P, Gouveia, Leonor, Kanna, Charan Raju, Wärmländer, Sebastian K T S, Platts, Jamie A, Kamerlin, Shina Caroline Lynn

Journal:

Year:

2014

Language:

english

File:

PDF, 964 KB

english, 2014

50

Understanding thio-effects in simple phosphoryl systems: role of solvent effects and nucleophile charge

Carvalho, Alexandra T. P., O'Donoghue, AnnMarie C., Hodgson, David R. W., Kamerlin, Shina C. L.

Journal:

Organic & Biomolecular Chemistry

Year:

2015

Language:

english

File:

PDF, 1.15 MB

english, 2015

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