Abhishek Singharoy

Asst Professor

  • 742 Citations
  • 16 h-Index
20072020

Research output per year

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Research Output

  • 742 Citations
  • 16 h-Index
  • 33 Article
  • 1 Chapter
  • 1 Review article
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Article
2019

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Singharoy, A., Maffeo, C., Delgado-Magnero, K. H., Swainsbury, D. J. K., Sener, M., Kleinekathöfer, U., Vant, J. W., Nguyen, J., Hitchcock, A., Isralewitz, B., Teo, I., Chandler, D. E., Stone, J. E., Phillips, J. C., Pogorelov, T. V., Mallus, M. I., Chipot, C., Luthey-Schulten, Z., Tieleman, D. P., Hunter, C. N. & 3 others, Tajkhorshid, E., Aksimentiev, A. & Schulten, K., Nov 14 2019, In : Cell. 179, 5, p. 1098-1111.e23

Research output: Contribution to journalArticle

9 Scopus citations
2018

Constructing atomic structural models into cryo-EM densities using molecular dynamics – Pros and cons

Wang, Y., Shekhar, M., Thifault, D., Williams, C. J., McGreevy, R., Richardson, J., Singharoy, A. & Tajkhorshid, E., Jan 1 2018, (Accepted/In press) In : Journal of Structural Biology.

Research output: Contribution to journalArticle

5 Scopus citations

Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem

Benson, C. R., Maffeo, C., Fatila, E. M., Liu, Y., Sheetz, E. G., Aksimentiev, A., Singharoy, A. & Flood, A. H., Sep 18 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 38, p. 9391-9396 6 p.

Research output: Contribution to journalArticle

5 Scopus citations
2017

CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments

Qi, Y., Lee, J., Singharoy, A., McGreevy, R., Schulten, K. & Im, W., Apr 20 2017, In : Journal of Physical Chemistry B. 121, 15, p. 3718-3723 6 p.

Research output: Contribution to journalArticle

8 Scopus citations

Chemomechanical coupling in hexameric protein-protein interfaces harnesses energy within V-type ATPases

Singharoy, A., Chipot, C., Moradi, M. & Schulten, K., Jan 11 2017, In : Journal of the American Chemical Society. 139, 1, p. 293-310 18 p.

Research output: Contribution to journalArticle

19 Scopus citations

Methodology for the Simulation of Molecular Motors at Different Scales

Singharoy, A. & Chipot, C., Apr 20 2017, In : Journal of Physical Chemistry B. 121, 15, p. 3502-3514 13 p.

Research output: Contribution to journalArticle

9 Scopus citations
2016

A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion

Botte, M., Zaccai, N. R., Nijeholt, J. L. À., Martin, R., Knoops, K., Papai, G., Zou, J., Deniaud, A., Karuppasamy, M., Jiang, Q., Roy, A. S., Schulten, K., Schultz, P., Rappsilber, J., Zaccai, G., Berger, I., Collinson, I. & Schaffitzel, C., Dec 7 2016, In : Scientific reports. 6, 38399.

Research output: Contribution to journalArticle

16 Scopus citations

Advances in the molecular dynamics flexible fitting method for cryo-EM modeling

McGreevy, R., Teo, I., Singharoy, A. & Schulten, K., May 1 2016, In : Methods. 100, p. 50-60 11 p.

Research output: Contribution to journalArticle

34 Scopus citations

Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing

Stone, J. E., Sener, M., Vandivort, K. L., Barragan, A., Singharoy, A., Teo, I., Ribeiro, J. V., Isralewitz, B., Liu, B., Goh, B. C., Phillips, J. C., MacGregor-Chatwin, C., Johnson, M. P., Kourkoutis, L. F., Hunter, C. N. & Schulten, K., Jul 2016, In : Parallel Computing. 55, p. 17-27 11 p.

Research output: Contribution to journalArticle

22 Scopus citations

Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2

Singharoy, A., Barragan, A. M., Thangapandian, S., Tajkhorshid, E. & Schulten, K., Sep 21 2016, In : Journal of the American Chemical Society. 138, 37, p. 12077-12089 13 p.

Research output: Contribution to journalArticle

5 Scopus citations

Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes

Goh, B. C., Hadden, J. A., Bernardi, R. C., Singharoy, A., McGreevy, R., Rudack, T., Cassidy, C. K. & Schulten, K., Jul 5 2016, In : Annual review of biophysics. 45, p. 253-278 26 p.

Research output: Contribution to journalArticle

34 Scopus citations

Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters

Bozzi, A. T., Bane, L. B., Weihofen, W. A., McCabe, A. L., Singharoy, A., Chipot, C. J., Schulten, K. & Gaudet, R., Sep 13 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 37, p. 10310-10315 6 p.

Research output: Contribution to journalArticle

24 Scopus citations

Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter

Bozzi, A. T., Bane, L. B., Weihofen, W. A., Singharoy, A., Guillen, E. R., Ploegh, H. L., Schulten, K. & Gaudet, R., Dec 6 2016, In : Structure. 24, 12, p. 2102-2114 13 p.

Research output: Contribution to journalArticle

14 Scopus citations

Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles

Liu, Y., Singharoy, A., Mayne, C. G., Sengupta, A., Raghavachari, K., Schulten, K. & Flood, A. H., Apr 27 2016, In : Journal of the American Chemical Society. 138, 14, p. 4843-4851 9 p.

Research output: Contribution to journalArticle

34 Scopus citations

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

Singharoy, A., Teo, I., McGreevy, R., Stone, J. E., Zhao, J. & Schulten, K., Jul 7 2016, In : eLife. 5, JULY, e16105.

Research output: Contribution to journalArticle

60 Scopus citations

Overall energy conversion efficiency of a photosynthetic vesicle

Sener, M., Strumpfer, J., Singharoy, A., Hunter, C. N. & Schulten, K., Aug 26 2016, In : eLife. 5, AUGUST, e09541.

Research output: Contribution to journalArticle

31 Scopus citations
2015

Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles

Singharoy, A., Venkatakrishnan, B., Liu, Y., Mayne, C. G., Lee, S., Chen, C. H., Zlotnick, A., Schulten, K. & Flood, A. H., Jul 15 2015, In : Journal of the American Chemical Society. 137, 27, p. 8810-8818 9 p.

Research output: Contribution to journalArticle

21 Scopus citations
2014

A structural model of the active ribosome-bound membrane protein insertase YidC

Wickles, S., Singharoy, A., Andreani, J., Seemayer, S., Bischoff, L., Berninghausen, O., Soeding, J., Schulten, K., van der Sluis, E. O. & Beckmann, R., Jul 10 2014, In : eLife. 3, July2014, p. 1-17 17 p., e03035.

Research output: Contribution to journalArticle

39 Scopus citations

Quasiequivalence of multiscale coevolution and ensemble MD simulations: A demonstration with lactoferrin

Yang, J., Singharoy, A., Sereda, Y. V. & Ortoleva, P. J., Nov 25 2014, In : Chemical Physics Letters. 616-617, p. 154-160 7 p.

Research output: Contribution to journalArticle

3 Scopus citations

Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain

Li, Q., Wanderling, S., Paduch, M., Medovoy, D., Singharoy, A., Mcgreevy, R., Villalba-Galea, C. A., Hulse, R. E., Roux, B., Schulten, K., Kossiakoff, A. & Perozo, E., Mar 2014, In : Nature Structural and Molecular Biology. 21, 3, p. 244-252 9 p.

Research output: Contribution to journalArticle

142 Scopus citations

XMDFF: Molecular dynamics flexible fitting of low-resolution X-ray structures

Mcgreevy, R., Singharoy, A., Li, Q., Zhang, J., Xu, D., Perozo, E. & Schulten, K., Aug 26 2014, In : Acta Crystallographica Section D: Biological Crystallography. 70, 9, p. 2344-2355 12 p.

Research output: Contribution to journalArticle

29 Scopus citations
2013

Epitope engineering and molecular metrics of immunogenicity: A computational approach to VLP-based vaccine design

Joshi, H., Lewis, K., Singharoy, A. & Ortoleva, P. J., Oct 1 2013, In : Vaccine. 31, 42, p. 4841-4847 7 p.

Research output: Contribution to journalArticle

13 Scopus citations

Epitope fluctuations in the human papillomavirus are under dynamic allosteric control: A computational evaluation of a new vaccine design strategy

Singharoy, A., Polavarapu, A., Joshi, H., Baik, M. H. & Ortoleva, P., Dec 11 2013, In : Journal of the American Chemical Society. 135, 49, p. 18458-18468 11 p.

Research output: Contribution to journalArticle

14 Scopus citations

Hierarchical multiscale modeling of macromolecules and their assemblies

Ortoleva, P., Singharoy, A. & Pankavich, S., Apr 28 2013, In : Soft Matter. 9, 16, p. 4319-4335 17 p.

Research output: Contribution to journalArticle

6 Scopus citations

Quasiperiodic oscillation and possible Second Law violation in a nanosystem

Quick, R., Singharoy, A. & Ortoleva, P., May 20 2013, In : Chemical Physics Letters. 571, p. 61-65 5 p.

Research output: Contribution to journalArticle

3 Scopus citations
2012

Discovering free energy basins for macromolecular systems via guided multiscale simulation

Sereda, Y. V., Singharoy, A. B., Jarrold, M. F. & Ortoleva, P. J., Jul 26 2012, In : Journal of Physical Chemistry B. 116, 29, p. 8534-8544 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

Hierarchical order parameters for macromolecular assembly simulations. 1. Construction and dynamical properties of order parameters

Singharoy, A., Sereda, Y. & Ortoleva, P. J., Apr 10 2012, In : Journal of Chemical Theory and Computation. 8, 4, p. 1379-1392 14 p.

Research output: Contribution to journalArticle

13 Scopus citations

Multiscale macromolecular simulation: Role of evolving ensembles

Singharoy, A., Joshi, H. & Ortoleva, P. J., Oct 22 2012, In : Journal of Chemical Information and Modeling. 52, 10, p. 2638-2649 12 p.

Research output: Contribution to journalArticle

10 Scopus citations

Space warping order parameters and symmetry: Application to multiscale simulation of macromolecular assemblies

Singharoy, A., Joshi, H., Miao, Y. & Ortoleva, P. J., Jul 26 2012, In : Journal of Physical Chemistry B. 116, 29, p. 8423-8434 12 p.

Research output: Contribution to journalArticle

16 Scopus citations
2011

Multiscale simulation of microbe structure and dynamics

Joshi, H., Singharoy, A., Sereda, Y. V., Cheluvaraja, S. C. & Ortoleva, P. J., Oct 1 2011, In : Progress in Biophysics and Molecular Biology. 107, 1, p. 200-217 18 p.

Research output: Contribution to journalArticle

26 Scopus citations

Order parameters for macromolecules: Application to multiscale simulation

Singharoy, A., Cheluvaraja, S. & Ortoleva, P., Jan 28 2011, In : Journal of Chemical Physics. 134, 4, 044104.

Research output: Contribution to journalArticle

28 Scopus citations
2010

Multiscale analytic continuation approach to nanosystem simulation: Applications to virus electrostatics

Singharoy, A., Yesnik, A. M. & Ortoleva, P., May 7 2010, In : Journal of Chemical Physics. 132, 17, 174112.

Research output: Contribution to journalArticle

9 Scopus citations
2007

Molecular tailoring and prediction of strongly ferromagnetically coupled trimethylenemethane-based nitroxide diradicals

Ali, M. E., Roy, A. S. & Datta, S. N., Jun 28 2007, In : Journal of Physical Chemistry A. 111, 25, p. 5523-5527 5 p.

Research output: Contribution to journalArticle

32 Scopus citations