My Publications
My publications
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2024
(3)
Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting.
Outhwaite, I. R; Singh, S.; Berger, B.; Knapp, S.; Chodera, J. D; and Seeliger, M. A
Elife, 12: e86189. 2024.
link bibtex
link bibtex
@article{outhwaite2024death,
title={Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting},
author={Outhwaite, Ian R and Singh, Sukrit and Berger, Benedict-Tilman and Knapp, Stefan and Chodera, John D and Seeliger, Markus A},
journal={Elife},
volume={12},
pages={e86189},
year={2024},
publisher={eLife Sciences Publications, Ltd}
}
Application of Established Computational Techniques to Identify Potential SARS-CoV-2 Nsp14-MTase Inhibitors in Low Data Regimes.
Nigam, A.; Hurley, M. F.; Lu, F.; Konkol'ová, E.; Klima, M.; Trylčová, J.; Pollice, R.; Cinaroglu, S. S.; Levin-Konigsberg, R.; Handjaya, J.; and others
Digital Discovery. 2024.
link bibtex
link bibtex
@article{nigam2024application,
title={Application of Established Computational Techniques to Identify Potential SARS-CoV-2 Nsp14-MTase Inhibitors in Low Data Regimes},
author={Nigam, AkshatKumar and Hurley, Matthew FD and Lu, Fengling and Konkol'ov{\'a}, Eva and Klima, Martin and Tryl{\v{c}}ov{\'a}, Jana and Pollice, Robert and Cinaroglu, Suleyman Selim and Levin-Konigsberg, Roni and Handjaya, Jasemine and others},
journal={Digital Discovery},
year={2024},
publisher={Royal Society of Chemistry}
}
G protein activation occurs via a largely universal mechanism.
Vithani, N.; Todd, T. D; Singh, S.; Trent, T.; Blumer, K. J; and Bowman, G. R
The Journal of Physical Chemistry B, 128(15): 3554–3562. 2024.
link bibtex
link bibtex
@article{vithani2024g,
title={G protein activation occurs via a largely universal mechanism},
author={Vithani, Neha and Todd, Tyson D and Singh, Sukrit and Trent, Tony and Blumer, Kendall J and Bowman, Gregory R},
journal={The Journal of Physical Chemistry B},
volume={128},
number={15},
pages={3554--3562},
year={2024},
publisher={American Chemical Society}
}
2023
(4)
Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein: protein complex.
Zhang, I.; Rufa, D. A; Pulido, I.; Henry, M. M; Rosen, L. E; Hauser, K.; Singh, S.; and Chodera, J. D
J. Chem. Theory Comput.,19–15. 2023.
link bibtex
link bibtex
@article{zhang2023identifying,
title={Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein: protein complex},
author={Zhang, Ivy and Rufa, Dominic A and Pulido, Iv{\'a}n and Henry, Michael M and Rosen, Laura E and Hauser, Kevin and Singh, Sukrit and Chodera, John D},
journal={J. Chem. Theory Comput.},
pages={19--15},
year={2023}
}
MEN1 mutations mediate clinical resistance to menin inhibition.
Perner, F.; Stein, E. M; Wenge, D. V; Singh, S.; Kim, J.; Apazidis, A.; Rahnamoun, H.; Anand, D.; Marinaccio, C.; Hatton, C.; and others
Nature, 615(7954): 913–919. 2023.
link bibtex
link bibtex
@article{perner2023men1,
title={MEN1 mutations mediate clinical resistance to menin inhibition},
author={Perner, Florian and Stein, Eytan M and Wenge, Daniela V and Singh, Sukrit and Kim, Jeonghyeon and Apazidis, Athina and Rahnamoun, Homa and Anand, Disha and Marinaccio, Christian and Hatton, Charlie and others},
journal={Nature},
volume={615},
number={7954},
pages={913--919},
year={2023},
publisher={Nature Publishing Group UK London}
}
Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.
Boby, M. L; Fearon, D.; Ferla, M.; Filep, M.; Koekemoer, L.; Robinson, M. C; Consortium‡, C. M.; Chodera, J. D; Lee, A. A; London, N.; and others
Science, 382(6671): eabo7201. 2023.
link bibtex
link bibtex
@article{boby2023open,
title={Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors},
author={Boby, Melissa L and Fearon, Daren and Ferla, Matteo and Filep, Mihajlo and Koekemoer, Lizb{\'e} and Robinson, Matthew C and COVID Moonshot Consortium‡ and Chodera, John D and Lee, Alpha A and London, Nir and others},
journal={Science},
volume={382},
number={6671},
pages={eabo7201},
year={2023},
publisher={American Association for the Advancement of Science}
}
Openmm 8: Molecular dynamics simulation with machine learning potentials.
Eastman, P.; Galvelis, R.; Peláez, R. P; Abreu, C. R.; Farr, S. E; Gallicchio, E.; Gorenko, A.; Henry, M. M; Hu, F.; Huang, J.; and others
The Journal of Physical Chemistry B, 128(1): 109–116. 2023.
link bibtex
link bibtex
@article{eastman2023openmm,
title={Openmm 8: Molecular dynamics simulation with machine learning potentials},
author={Eastman, Peter and Galvelis, Raimondas and Pel{\'a}ez, Ra{\'u}l P and Abreu, Charlles RA and Farr, Stephen E and Gallicchio, Emilio and Gorenko, Anton and Henry, Michael M and Hu, Frank and Huang, Jing and others},
journal={The Journal of Physical Chemistry B},
volume={128},
number={1},
pages={109--116},
year={2023},
publisher={ACS Publications}
}
2021
(5)
The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA.
Cubuk, J.; Alston, J. J; Incicco, J J.; Singh, S.; Stuchell-Brereton, M. D; Ward, M. D; Zimmerman, M. I; Vithani, N.; Griffith, D.; Wagoner, J. A; and others
Nature Communications, 12(1): 1–17. 2021.
link bibtex
link bibtex
@article{cubuk2021sars,
title={The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA},
author={Cubuk, Jasmine and Alston, Jhullian J and Incicco, J Jerem{\'\i}as and Singh, Sukrit and Stuchell-Brereton, Melissa D and Ward, Michael D and Zimmerman, Maxwell I and Vithani, Neha and Griffith, Daniel and Wagoner, Jason A and others},
journal={Nature Communications},
volume={12},
number={1},
pages={1--17},
year={2021},
publisher={Nature Publishing Group}
}
SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential.
Vithani, N.; Ward, M. D; Zimmerman, M. I; Novak, B.; Borowsky, J. H; Singh, S.; and Bowman, G. R
Biophysical Journal, 120(14): 2880–2889. 2021.
link bibtex
link bibtex
@article{vithani2021sars,
title={SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential},
author={Vithani, Neha and Ward, Michael D and Zimmerman, Maxwell I and Novak, Borna and Borowsky, Jonathan H and Singh, Sukrit and Bowman, Gregory R},
journal={Biophysical Journal},
volume={120},
number={14},
pages={2880--2889},
year={2021},
publisher={Cell Press}
}
SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome.
Zimmerman, M. I; Porter, J. R; Ward, M. D; Singh, S.; Vithani, N.; Meller, A.; Mallimadugula, U. L; Kuhn, C. E; Borowsky, J. H; Wiewiora, R. P; and others
Nature chemistry, 13(7): 651–659. 2021.
link bibtex
link bibtex
@article{zimmerman2021sars,
title={SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome},
author={Zimmerman, Maxwell I and Porter, Justin R and Ward, Michael D and Singh, Sukrit and Vithani, Neha and Meller, Artur and Mallimadugula, Upasana L and Kuhn, Catherine E and Borowsky, Jonathan H and Wiewiora, Rafal P and others},
journal={Nature chemistry},
volume={13},
number={7},
pages={651--659},
year={2021},
publisher={Nature Publishing Group}
}
A cryptic pocket in Ebola VP35 allosterically controls RNA binding.
Cruz, M. A; Frederick, T. E; Mallimadugula, U.; Singh, S.; Vithani, N.; Zimmerman, M. I; Porter, J. R; Moeder, K. E; Amarasinghe, G. K; and Bowman, G. R
Nature Communications, 13(2269). 2021.
link bibtex
link bibtex
@article{cruz2021cryptic,
title={A cryptic pocket in Ebola VP35 allosterically controls RNA binding},
author={Cruz, Matthew A and Frederick, Thomas E and Mallimadugula, Upasana and Singh, Sukrit and Vithani, Neha and Zimmerman, Maxwell I and Porter, Justin R and Moeder, Katelyn E and Amarasinghe, Gaya K and Bowman, Gregory R},
journal={Nature Communications},
volume={13},
number={2269},
year={2021}
}
Opening of a cryptic pocket in β-lactamase increases penicillinase activity.
Knoverek, C.; Mallimadugula, U.; Singh, S; Renella, E; Frederick, T.; Yuwen, T; Raavicharla, S; Kay, L.; and Bowman, G.
Proceedings of the National Academy of Sciences, 118(47). 2021.
link bibtex
link bibtex
@article{knoverek2021opening,
title={Opening of a cryptic pocket in $\beta$-lactamase increases penicillinase activity},
author={Knoverek, CR and Mallimadugula, UL and Singh, S and Renella, E and Frederick, TE and Yuwen, T and Raavicharla, S and Kay, LE and Bowman, GR},
journal={Proceedings of the National Academy of Sciences},
volume={118},
number={47},
year={2021}
}
2020
(2)
Antagonism between substitutions in β-lactamase explains a path not taken in the evolution of bacterial drug resistance.
Brown, C. A; Hu, L.; Sun, Z.; Patel, M. P; Singh, S.; Porter, J. R; Sankaran, B.; Prasad, B. V.; Bowman, G. R; and Palzkill, T.
Journal of Biological Chemistry, 295(21): 7376–7390. 2020.
link bibtex
link bibtex
@article{brown2020antagonism,
title={Antagonism between substitutions in $\beta$-lactamase explains a path not taken in the evolution of bacterial drug resistance},
author={Brown, Cameron A and Hu, Liya and Sun, Zhizeng and Patel, Meha P and Singh, Sukrit and Porter, Justin R and Sankaran, Banumathi and Prasad, BV Venkataram and Bowman, Gregory R and Palzkill, Timothy},
journal={Journal of Biological Chemistry},
volume={295},
number={21},
pages={7376--7390},
year={2020},
publisher={Elsevier}
}
Understanding and Exploiting Protein Allostery and Dynamics Using Molecular Simulations.
Singh, S.
Ph.D. Thesis, Washington University in St. Louis, 2020.
link bibtex
link bibtex
@phdthesis{singh2020understanding,
title={Understanding and Exploiting Protein Allostery and Dynamics Using Molecular Simulations},
author={Singh, Sukrit},
year={2020},
school={Washington University in St. Louis}
}
2018
(3)
Mechanistic Basis for ATP-Dependent Inhibition of Glutamine Synthetase by Tabtoxinine-β-lactam.
Patrick, G. J; Fang, L.; Schaefer, J.; Singh, S.; Bowman, G. R; and Wencewicz, T. A
Biochemistry, 57(1): 117–135. 2018.
link bibtex
link bibtex
@article{patrick2018mechanistic,
title={Mechanistic Basis for ATP-Dependent Inhibition of Glutamine Synthetase by Tabtoxinine-$\beta$-lactam},
author={Patrick, Garrett J and Fang, Luting and Schaefer, Jacob and Singh, Sukrit and Bowman, Gregory R and Wencewicz, Timothy A},
journal={Biochemistry},
volume={57},
number={1},
pages={117--135},
year={2018},
publisher={American Chemical Society}
}
Design, synthesis, and biological evaluation of stable β6. 3-Helices: Discovery of non-hemolytic antibacterial peptides.
Reddy, D. N; Singh, S.; Ho, C. M.; Patel, J.; Schlesinger, P.; Rodgers, S.; Doctor, A.; and Marshall, G. R
European journal of medicinal chemistry, 149: 193–210. 2018.
link bibtex
link bibtex
@article{reddy2018design,
title={Design, synthesis, and biological evaluation of stable $\beta$6. 3-Helices: Discovery of non-hemolytic antibacterial peptides},
author={Reddy, Damodara N and Singh, Sukrit and Ho, Chris MW and Patel, Janki and Schlesinger, Paul and Rodgers, Stephen and Doctor, Allan and Marshall, Garland R},
journal={European journal of medicinal chemistry},
volume={149},
pages={193--210},
year={2018},
publisher={Elsevier Masson}
}
Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding.
Sun, X.; Singh, S.; Blumer, K. J; and Bowman, G. R
eLife, 7: e38465. 2018.
link bibtex 1 download
link bibtex 1 download
@article{sun2018simulation,
title={Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding},
author={Sun, Xianqiang and Singh, Sukrit and Blumer, Kendall J and Bowman, Gregory R},
journal={eLife},
volume={7},
pages={e38465},
year={2018}
}
2017
(3)
Dexmedetomidine protects against glucocorticoid induced progenitor cell apoptosis in neonatal mouse cerebellum.
O’Connor, S. D.; Cabrera, O. H.; Dougherty, J. D; Singh, S.; Swiney, B. S.; Salinas-Contreras, P.; Farber, N. B.; and Noguchi, K. K.
The Journal of Maternal-Fetal & Neonatal Medicine, 30(18): 2156–2162. 2017.
link bibtex
link bibtex
@article{o2017dexmedetomidine,
title={Dexmedetomidine protects against glucocorticoid induced progenitor cell apoptosis in neonatal mouse cerebellum},
author={O’Connor, Shawn David and Cabrera, Omar Hose{\'a} and Dougherty, Joseph D and Singh, Sukrit and Swiney, Brant Stephen and Salinas-Contreras, Patricia and Farber, Nuri Bradford and Noguchi, Kevin Kiyoshi},
journal={The Journal of Maternal-Fetal \& Neonatal Medicine},
volume={30},
number={18},
pages={2156--2162},
year={2017},
publisher={Taylor \& Francis}
}
The small molecule JIB-04 disrupts O 2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A.
Cascella, B.; Lee, S. G.; Singh, S.; Jez, J. M; and Mirica, L. M
Chemical Communications, 53(13): 2174–2177. 2017.
link bibtex
link bibtex
@article{cascella2017small,
title={The small molecule JIB-04 disrupts O 2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A},
author={Cascella, Barbara and Lee, Soon Goo and Singh, Sukrit and Jez, Joseph M and Mirica, Liviu M},
journal={Chemical Communications},
volume={53},
number={13},
pages={2174--2177},
year={2017},
publisher={Royal Society of Chemistry}
}
Quantifying allosteric communication via both concerted structural changes and conformational disorder with CARDS.
Singh, S.; and Bowman, G. R
Journal of Chemical Theory and Computation, 13(4): 1509–1517. 2017.
link bibtex
link bibtex
@article{singh2017quantifying,
title={Quantifying allosteric communication via both concerted structural changes and conformational disorder with CARDS},
author={Singh, Sukrit and Bowman, Gregory R},
journal={Journal of Chemical Theory and Computation},
volume={13},
number={4},
pages={1509--1517},
year={2017},
publisher={American Chemical Society}
}
2016
(1)
Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor.
Brosey, C. A; Ho, C.; Long, W. Z; Singh, S.; Burnett, K.; Hura, G. L; Nix, J. C; Bowman, G. R; Ellenberger, T.; and Tainer, J. A
Structure, 24(12): 2067–2079. 2016.
link bibtex
link bibtex
@article{brosey2016defining,
title={Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor},
author={Brosey, Chris A and Ho, Chris and Long, Winnie Z and Singh, Sukrit and Burnett, Kathryn and Hura, Greg L and Nix, Jay C and Bowman, Gregory R and Ellenberger, Tom and Tainer, John A},
journal={Structure},
volume={24},
number={12},
pages={2067--2079},
year={2016},
publisher={Cell Press}
}
2015
(1)
Structural conservation and functional diversity of the poxvirus immune evasion (PIE) domain superfamily.
Nelson, C. A; Epperson, M. L; Singh, S.; Elliott, J. I; and Fremont, D. H
Viruses, 7(9): 4873–4893. 2015.
link bibtex
link bibtex
@article{nelson2015structural,
title={Structural conservation and functional diversity of the poxvirus immune evasion (PIE) domain superfamily},
author={Nelson, Christopher A and Epperson, Megan L and Singh, Sukrit and Elliott, Jabari I and Fremont, Daved H},
journal={Viruses},
volume={7},
number={9},
pages={4873--4893},
year={2015},
publisher={Multidisciplinary Digital Publishing Institute}
}
2014
(2)
Lithium protects against glucocorticoid induced neural progenitor cell apoptosis in the developing cerebellum.
Cabrera, O.; Dougherty, J.; Singh, S.; Swiney, B. S; Farber, N. B; and Noguchi, K. K
Brain research, 1545: 54–63. 2014.
link bibtex
link bibtex
@article{cabrera2014lithium,
title={Lithium protects against glucocorticoid induced neural progenitor cell apoptosis in the developing cerebellum},
author={Cabrera, Omar and Dougherty, Joseph and Singh, Sukrit and Swiney, Brant S and Farber, Nuri B and Noguchi, Kevin K},
journal={Brain research},
volume={1545},
pages={54--63},
year={2014},
publisher={Elsevier}
}
Synthesis of Amide Bond Nitroxide for Determination of Intermolecular Distances in HIV Initiation.
Singh, S.
. 2014.
link bibtex
link bibtex
@article{singh2014synthesis,
title={Synthesis of Amide Bond Nitroxide for Determination of Intermolecular Distances in HIV Initiation},
author={Singh, Sukrit},
year={2014}
}