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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

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

4

Computer simulation of protein folding

Levitt, Michael, Warshel, Arieh

Journal:

Year:

1975

File:

PDF, 542 KB

1975

5

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

6

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

7

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

8

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

9

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

10

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

11

The low barrier hydrogen bond (LBHB) proposal revisited: The case of the Asp ··· His pair in serine proteases

Claudia N. Schutz, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 220 KB

english, 2004

12

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

13

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

14

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

15

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

16

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

17

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

18

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

19

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

20

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

21

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

22

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

23

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

24

Effective way of modeling chemical catalysis: Empirical valence bond picture of role of solvent and catalyst in alkylation reactions

Vill�, Jordi, Bentzien, J�rg, Gonz�lez-Lafont, �ngels, Lluch, Jos� M., Bertran, Juan, Warshel, Arieh

Journal:

Journal of Computational Chemistry

Year:

2000

Language:

english

File:

PDF, 429 KB

english, 2000

25

Electrostatic contributions to protein–protein binding affinities: Application to Rap/Raf interaction

Ingo Muegge, Thomas Schweins, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1998

Language:

english

File:

PDF, 271 KB

english, 1998

26

Simulating proton translocations in proteins: Probing proton transfer pathways in the Rhodobacter sphaeroides reaction center

Yuk Yin Sham, Ingo Muegge, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 346 KB

english, 1999

27

Ab initio/LD studies of chemical reactions in solution: Reference free-energy surfaces for acylation reactions occurring in serine and cysteine proteases

Marek Štrajbl, Jan Florián, Arieh Warshel

Journal:

International Journal of Quantum Chemistry

Year:

2000

Language:

english

File:

PDF, 411 KB

english, 2000

28

Constraining the electron densities in DFT method as an effective way for ab initio studies of metal-catalyzed reactions

Gongyi Hong, Marek Strajbl, Tomasz A. Wesolowski, Arieh Warshel

Journal:

Journal of Computational Chemistry

Year:

2000

Language:

english

File:

PDF, 377 KB

english, 2000

29

Circe Effect versus Enzyme Preorganization: What Can Be Learned from the Structure of the Most Proficient Enzyme?

Arieh Warshel, Jan Florián, Marek Štrajbl, Jordi Villà

Journal:

Year:

2001

Language:

english

File:

PDF, 69 KB

english, 2001

30

Predicting Drug-Resistant Mutations of HIV Protease

Hiroshi Ishikita, Arieh Warshel

Journal:

Angewandte Chemie

Year:

2008

Language:

english

File:

PDF, 551 KB

english, 2008

31

Predicting Drug-Resistant Mutations of HIV Protease

Hiroshi Ishikita, Arieh Warshel

Journal:

Angewandte Chemie International Edition

Year:

2008

Language:

english

File:

PDF, 551 KB

english, 2008

32

Computer simulation studies of the fidelity of DNA polymerases

Jan Florián, Myron F. Goodman, Arieh Warshel

Journal:

Year:

2003

Language:

english

File:

PDF, 815 KB

english, 2003

33

On the Generation of Catalytic Antibodies by Transition State Analogues

Montserrat Barbany, Hugo Gutiérrez-de-Terán, Ferran Sanz, Jordi Villà-Freixa, Arieh Warshel

Journal:

Year:

2003

Language:

english

File:

PDF, 180 KB

english, 2003

34

Towards Quantitative Computer-Aided Studies of Enzymatic Enantioselectivity: The Case of Candida antarctica Lipase A

Maria P. Frushicheva, Prof. Dr. Arieh Warshel

Journal:

Year:

2012

Language:

english

File:

PDF, 713 KB

english, 2012

35

ChemInform Abstract: Molecular Dynamics Simulations of Biological Reactions

Journal:

Year:

2002

File:

PDF, 23 KB

2002

36

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

37

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

38

Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs

Frederick S. Lee, Zhen Tao Chu, Arieh Warshel

Journal:

Journal of Computational Chemistry

Year:

1993

Language:

english

File:

PDF, 2.46 MB

english, 1993

39

The resonance Raman spectrum of azulene

Ranty Liang, Otto Schnepp, Arieh Warshel

Journal:

Chemical Physics Letters

Year:

1976

Language:

english

File:

PDF, 506 KB

english, 1976

40

On the molecular origin of the anomalous polarization in the resonance raman of metalloporphyrins

Journal:

Chemical Physics Letters

Year:

1976

Language:

english

File:

PDF, 619 KB

english, 1976

41

Semiclassical simulations of the spectra of anharmonic molecules; problems and alternatives

Jenn-Kang Hwang, Arieh Warshel

Journal:

Chemical Physics Letters

Year:

1985

Language:

english

File:

PDF, 448 KB

english, 1985

42

A shortcut for multidimensional quantization. The average partial actions method

Jenn-Kang Hwang, Arieh Warshel

Journal:

Chemical Physics Letters

Year:

1985

Language:

english

File:

PDF, 416 KB

english, 1985

43

The QCFF/PI+MCA program package efficiency and versatility in molecular mechanics

Journal:

Computers & Chemistry

Year:

1977

Language:

english

File:

PDF, 706 KB

english, 1977

44

Combined AB initio and electrostatic calculations of tryptophan-191 oxidation in compound ES of cytochrome-c-peroxidase

Steven W. Bunte, Gerard M. Jensen, Arieh Warshel, David B. Goodin

Journal:

Journal of Inorganic Biochemistry

Year:

1995

Language:

english

File:

PDF, 55 KB

english, 1995

45

Theoretical evaluation of potential surfaces, equilibrium geometries and vibronic transition intensities of excimers: the pyrene crystal excimer

Arieh Warshel, Eduardo Huler

Journal:

Chemical Physics

Year:

1974

Language:

english

File:

PDF, 473 KB

english, 1974

46

Resonance raman spectrum of azulene

Ranty Liang, Otto Schnepp, Arieh Warshel

Journal:

Chemical Physics

Year:

1978

Language:

english

File:

PDF, 767 KB

english, 1978

47

Modeling electrostatic effects in proteins

Arieh Warshel, Pankaz K. Sharma, Mitsunori Kato, William W. Parson

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2006

Language:

english

File:

PDF, 1.74 MB

english, 2006

48

A density-matrix model of photosynthetic electron transfer with microscopically estimated vibrational relaxation times

William W. Parson, Arieh Warshel

Journal:

Chemical Physics

Year:

2004

Language:

english

File:

PDF, 542 KB

english, 2004

49

Mechanistic alternatives in phosphate monoester hydrolysis: What conclusions can be drawn from available experimental data?

Johan Åqvist, Karin Kolmodin, Jan Florian, Arieh Warshel

Journal:

Chemistry & Biology

Year:

1999

Language:

english

File:

PDF, 1.29 MB

english, 1999

50

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

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