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1

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

2

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

3

Non-Canonical Base Pairs and Higher Order Structures in Nucleic Acids: Crystal Structure Database Analysis

Das, Jhuma, Mukherjee, Shayantani, Mitra, Abhijit, Bhattacharyya, Dhananjay

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2006

Language:

english

File:

PDF, 2.23 MB

english, 2006

4

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

5

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

6

Electrostatic Basis of the Unidirectional Walking Motion in Myosin Molecular Motors

Mukherjee, Shayantani, Warshel, Arieh

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 61 KB

english, 2014

7

Brønsted slopes based on single-molecule imaging data help to unveil the chemically coupled rotation in F 1 -ATPase

Mukherjee, Shayantani, Warshel, Arieh

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 744 KB

english, 2015

8

Role of Electrostatics in the Mechanochemical Rotary Mechanism of F1-ATPase

Mukherjee, Shayantani, Warshel, Arieh

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 60 KB

english, 2012

9

Concentration-Dependent Association between Weakly Attractive Nanoparticles in Aqueous Solutions

Sharmah, Arjun, Mukherjee, Shayantani, Yao, Zi, Lu, Lei, Guo, Ting

Journal:

The Journal of Physical Chemistry C

Year:

2016

Language:

english

File:

PDF, 2.62 MB

english, 2016

10

Conformational Change in MSH2-MSH6 upon Binding DNA Coupled to ATPase Activity

Mukherjee, Shayantani, Feig, Michael

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 652 KB

english, 2009

11

Electrostatic Origin of the Catalytic Effect of a Supramolecular Host Catalyst

Frushicheva, Maria P., Mukherjee, Shayantani, Warshel, Arieh

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 1.34 MB

english, 2012

12

Effect of phosphorothioate chirality on the grooves of DNA double helices: A molecular dynamics study

Shayantani Mukherjee, Dhananjay Bhattacharyya

Journal:

Year:

2004

Language:

english

File:

PDF, 453 KB

english, 2004

13

Deciphering the Mismatch Recognition Cycle in MutS and MSH2-MSH6 Using Normal-Mode Analysis

Mukherjee, Shayantani, Law, Sean M., Feig, Michael

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 3.22 MB

english, 2009

14

PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

Srinivasa M. Gopal, Shayantani Mukherjee, Yi-Ming Cheng, Michael Feig

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 871 KB

english, 2010

15

PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

Srinivasa M. Gopal, Shayantani Mukherjee, Yi-Ming Cheng, Michael Feig

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 36 KB

english, 2010

16

DNA Bending Propensity in the Presence of Base Mismatches: Implications for DNA Repair

Sharma, Monika, Predeus, Alexander V., Mukherjee, Shayantani, Feig, Michael

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 4.22 MB

english, 2013

17

Molecular Mechanism by Which Palmitate Inhibits PKR Autophosphorylation

Cho, Hyunju, Mukherjee, Shayantani, Palasuberniam, Pratheeba, Pillow, Lisa, Bilgin, Betul, Nezich, Catherine, Walton, S. Patrick, Feig, Michael, Chan, Christina

Journal:

Year:

2011

Language:

english

File:

PDF, 3.55 MB

english, 2011

18

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

Shayantani Mukherjee and Arieh Warshel

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.61 MB

english, 2011

19

Role of the Central Stalk in the Rotary-Chemical Coupling and Torque Generation of F1-ATPase

Mukherjee, Shayantani, Warshel, Arieh

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 38 KB

english, 2016

20

Simulating the dynamics of the mechanochemical cycle of myosin-V

Mukherjee, Shayantani, Alhadeff, Raphael, Warshel, Arieh

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 1.15 MB

english, 2017

21

DNA Bending and Discrimination of Mismatches by MutS and Human Homologs

Feig, Michael, Sharma, Monika, Predeus, Alexander, Mukherjee, Shayantani, Kovacs, Nicholas

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 127 KB

english, 2014

22

The FOF1 ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function

Mukherjee, Shayantani, Warshel, Arieh

Journal:

Photosynthesis Research

Year:

2017

Language:

english

File:

PDF, 9.26 MB

english, 2017

23

Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis

Shayantani Mukherjee, Manju Bansal, Dhananjay Bhattacharyya

Journal:

Journal of Computer-Aided Molecular Design

Year:

2006

Language:

english

File:

PDF, 593 KB

english, 2006

24

Mismatch Recognition Cycle in MutS and MSH2-MSH6 from Normal Mode Analysis and Simulations

Mukherjee, Shayantani, Law, Sean M., Feig, Michael

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 116 KB

english, 2009

25

Role of Hydrogen Bonds in Protein−DNA Recognition: Effect of Nonplanar Amino Groups

Mukherjee, Shayantani, Majumdar, Sudipta, Bhattacharyya, Dhananjay

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 481 KB

english, 2005

26

Realistic Modeling of Biological Motors; Electrostatic Origin of the Mechnochemical Rotatory Mechanism and the Catalytic Dwell of F1-ATPase

Warshel, Arieh, Mukherjee, Shayantani

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 40 KB

english, 2012

27

Simulating the Pulling of Stalled Elongated Peptide from the Ribosome by the Translocon

Rychkova, Anna, Mukherjee, Shayantani, Bora, Ram P., Warshel, Arieh

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 61 KB

english, 2014

28

10 How is fidelity maintained in nucleic acids? Two tales in DNA repair and DNA transcription from computer simulations

Feig, Michael, Wang, Beibei, Sharma, Monika, Burton, Zachary, Opron, Kristopher, Cukier, Robert, Predeus, Alexander, Kovacs, Nicholas, Law, Sean, Mukherjee, Shayantani

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2015

Language:

english

File:

PDF, 759 KB

english, 2015

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