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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

Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

A. Warshel, M. Levitt

Journal:

Journal of Molecular Biology

Year:

1976

Language:

english

File:

PDF, 3.17 MB

english, 1976

4

The Physics and Physical Chemistry of Molecular Machines

Astumian, R. Dean, Mukherjee, Shayantani, Warshel, Arieh

Journal:

Year:

2016

Language:

english

File:

PDF, 4.22 MB

english, 2016

5

On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes

Alexandra Vardi Kilshtain, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 323 KB

english, 2009

6

Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture)

Journal:

Angewandte Chemie International Edition

Year:

2014

Language:

english

File:

PDF, 2.73 MB

english, 2014

7

Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization

Lameira, Jeronimo, Bora, Ram Prasad, Chu, Zhen T., Warshel, Arieh

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 495 KB

english, 2015

8

Quantum Mechanical Consistent Force Field (QCFF/PI) Method: Calculations of Energies, Conformations and Vibronic Interactions of Ground and Excited States of Conjugated Molecules

Journal:

Israel Journal of Chemistry

Year:

1973

Language:

english

File:

PDF, 649 KB

english, 1973

9

Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches

Aaqvist, Johan., Warshel, Arieh.

Journal:

Chemical Reviews

Year:

1993

Language:

english

File:

PDF, 4.38 MB

english, 1993

10

Computer simulation of protein folding

Levitt, Michael, Warshel, Arieh

Journal:

Year:

1975

File:

PDF, 542 KB

1975

11

Electrostatic Basis for Enzyme Catalysis

Warshel, Arieh, Sharma, Pankaz K., Kato, Mitsunori, Xiang, Yun, Liu, Hanbin, Olsson, Mats H. M.

Journal:

Chemical Reviews

Year:

2006

Language:

english

File:

PDF, 847 KB

english, 2006

12

Critical Differences Between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV

Bai, Chen, Warshel, Arieh

Journal:

Journal of Physical Chemistry B

Year:

2020

File:

PDF, 1.30 MB

2020

13

Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease

Yuk Yin Sham, Zhen Tao Chu, Holly Tao, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 202 KB

english, 2000

14

What are the dielectric “constants” of proteins and how to validate electrostatic models?

Claudia N. Schutz, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 393 KB

english, 2001

15

Long-term Outcomes for Teen Mothers Who Participated in a Mentoring Program to Prevent Repeat Teen Pregnancy

Lin, Chyongchiou Jeng, Nowalk, Mary Patricia, Ncube, Collette N., Aaraj, Yassmin AL., Warshel, McKenzie, South-Paul, Jeannette E.

Journal:

Journal of the National Medical Association

Year:

2018

Language:

english

File:

PDF, 161 KB

english, 2018

16

Frozen density functional approach for ab initio calculations of solvated molecules

Wesolowski, Tomasz Adam, Warshel, Arieh

Journal:

Journal of Physical Chemistry

Year:

1993

Language:

english

File:

PDF, 445 KB

english, 1993

17

Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights

Journal:

Annual Review of Biophysics and Biomolecular Structure

Year:

2003

Language:

english

File:

PDF, 231 KB

english, 2003

18

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

19

How do serine proteases really work?

Warshel, A., Naray-Szabo, G., Sussman, F., Hwang, J. K.

Journal:

Year:

1989

Language:

english

File:

PDF, 3.29 MB

english, 1989

20

Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome

Adamczyk, A. J., Warshel, A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 953 KB

english, 2011

21

Quantum Catalysis in Enzymes: Beyond the Transition State Theory || Transition State Theory Can Be Used in Studies of Enzyme Catalysis: Lessons from Simulations of Tunnelling and Dynamical Effects in Lipoxygenase and Other Systems

Mats H. M. Olsson, Janez Mavri and Arieh Warshel

Journal:

Philosophical Transactions Biological Sciences

Year:

2006

Language:

english

File:

PDF, 3.69 MB

english, 2006

22

Consistent Force Field Calculations. II. Crystal Structures, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations, and Enthalpies of Alkanes

Journal:

The Journal of Chemical Physics

Year:

1970

Language:

english

File:

PDF, 1.14 MB

english, 1970

23

Dynamics of biochemical and biophysical reactions: insight from computer simulations

Warshel, Arieh, W. Parson, William

Journal:

Quarterly Reviews of Biophysics

Year:

2001

Language:

english

File:

PDF, 3.71 MB

english, 2001

24

Torque, chemistry and efficiency in molecular motors: a study of the rotary–chemical coupling in F1-ATPase

Mukherjee, Shayantani, Bora, Ram Prasad, Warshel, Arieh

Journal:

Quarterly Reviews of Biophysics

Year:

2015

Language:

english

File:

PDF, 597 KB

english, 2015

25

Electrostatic Energy and Macromolecular Function

Warshel, A, Aqvist, J

Journal:

Annual Review of Biophysics and Bioengineering

Year:

1991

Language:

english

File:

PDF, 853 KB

english, 1991

26

The barrier for proton transport in aquaporins as a challenge for electrostatic models: The role of protein relaxation in mutational calculations

Mitsunori Kato, Andrei V. Pisliakov, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 648 KB

english, 2006

27

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

28

Validating the vitality strategy for fighting drug resistance

Nidhi Singh, Maria P. Frushicheva, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.29 MB

english, 2012

29

Exploring the origin of the ion selectivity of the KcsA potassium channel

Anton Burykin, Mitsunori Kato, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 1.01 MB

english, 2003

30

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

31

ChemInform Abstract: Protein Control of Redox Potentials of Iron-Sulfur Proteins

P. J. STEPHENS, D. R. JOLLIE, A. WARSHEL

Journal:

Year:

1997

File:

PDF, 24 KB

1997

32

Semiclassical trajectory approach to photoisomerization

A. Warshel, M. Karplus

Journal:

Chemical Physics Letters

Year:

1975

Language:

english

File:

PDF, 763 KB

english, 1975

33

A comprehensive examination of the contributions to the binding entropy of protein–ligand complexes

Nidhi Singh, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 413 KB

english, 2010

34

The empirical valence bond as an effective strategy for computer-aided enzyme design

Alexandra Vardi-Kilshtain, Maite Roca, Arieh Warshel

Journal:

Biotechnology Journal

Year:

2009

Language:

english

File:

PDF, 199 KB

english, 2009

35

EMPIRICAL VALENCE BOND CALCULATIONS OF ENZYME CATALYSIS

A. Warshel, R. M. Weiss

Journal:

Annals of the New York Academy of Sciences

Year:

1981

Language:

english

File:

PDF, 708 KB

english, 1981

36

Computer Simulations of Enzyme Catalysis: Finding out what has been Optimized by Evolution

Arieh Warshel and Jan Florian

Journal:

Proceedings of the National Academy of Sciences

Year:

1998

Language:

english

File:

PDF, 1.13 MB

english, 1998

37

Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B

Schopf, Patrick, Warshel, Arieh

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 490 KB

english, 2014

38

An effective Coarse-grained model for biological simulations: Recent refinements and validations

Vicatos, Spyridon, Rychkova, Anna, Mukherjee, Shayantani, Warshel, Arieh

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 999 KB

english, 2014

39

On the Reactivity of Phosphate Monoester Dianions in Aqueous Solution: Brønsted Linear Free-Energy Relationships Do Not Have an Unique Mechanistic Interpretation

Florián, Jan, Åqvist, Johan, Warshel, Arieh

Journal:

Journal of the American Chemical Society

Year:

1998

Language:

english

File:

PDF, 44 KB

english, 1998

40

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

41

Calculations of enzymic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes

Journal:

Year:

1981

Language:

english

File:

PDF, 2.02 MB

english, 1981

42

Toward Accurate Screening in Computer-Aided Enzyme Design †

Roca, Maite, Vardi-Kilshtain, Alexandra, Warshel, Arieh

Journal:

Year:

2009

Language:

english

File:

PDF, 2.20 MB

english, 2009

43

On the mechanism of guanosine triphosphate hydrolysis in ras p21 proteins

Langen, Ralf, Schweins, Thomas, Warshel, Arieh

Journal:

Year:

1992

Language:

english

File:

PDF, 2.33 MB

english, 1992

44

How important are entropic contributions to enzyme catalysis?

Villa, J., Strajbl, M., Glennon, T. M., Sham, Y. Y., Chu, Z. T., Warshel, A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2000

Language:

english

File:

PDF, 272 KB

english, 2000

45

Dissecting the role of the γ-subunit in the rotary–chemical coupling and torque generation of F 1 -ATPase

Mukherjee, Shayantani, Warshel, Arieh

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.62 MB

english, 2015

46

Toward computer-aided site-directed mutagenesis of enzymes.

Warshel, A., Sussman, F.

Journal:

Proceedings of the National Academy of Sciences

Year:

1986

Language:

english

File:

PDF, 993 KB

english, 1986

47

ChemInform Abstract: Theoretical Correlation of Structure and Energetics in the Catalytic Reaction of Trypsin.

WARSHEL, A., RUSSELL, S.

Journal:

Year:

1987

File:

PDF, 106 KB

1987

48

Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β

Matute, Ricardo A., Yoon, Hanwool, Warshel, Arieh

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.61 MB

english, 2016

49

[Methods in Enzymology] Biomembranes Part O: Protons and Water: Structure and Translocation Volume 127 || [42] Correlation between the structure and efficiency of light-induced proton pumps

Year:

1986

Language:

english

File:

PDF, 461 KB

english, 1986

50

Exploring the catalytic mechanism of Cas9 using information inferred from Endonuclease VII

Yoon, Hanwool, Zhao, Li Na, Warshel, Arieh

Journal:

Year:

2018

Language:

english

File:

PDF, 1010 KB

english, 2018

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