Under review:
1. Chmielewski, D.; Wilson, E.; Pintilie, G.; Zhao, P.; Chen, M.; Schmid,M.F.; Simmons, G.; Wells, L.; Jing,J.; Singharoy, A.* ; Chiu, W.* Integrated analyses reveal a hinge glycan regulates coronavirus spike tilting and virus infectivity. Nature Comm (major revision) doi: 10.21203/rs.3.rs-2553619/v1
2. Sokolova, V.; Miratski, J., Singharoy, A.; Tan, D. Structure of human HP1⍺ in complex with H2A.Z nucleosome. Nature (major revision).
3. Wilson, E.; Cava, J. K.; Chowell, D.; Anderson, K.; Singharoy A.* The electrostatic landscape of MHC-peptide binding revealed using inception networks. Cell Systems (major revision).
4. Wang, H. ; Vant,J.; Wu, Y.; Sánchez R.; Micou, M.L.; Zhang,A.; Luczak, V.; Blenda, S.Y.; Jabbo, M.; Yoon, S.; Abdallah, A.; Ghassemian, M.; Griffis, E.; Hammarlund, M.; Singharoy, A.; Pekkurnaz, A. “Glycolytic metabolon assembly on mitochondria via Hexokinase O-GlcNAcylation”. Cell Metabolism (submitted).

2023:
Sarkar, D.; Lee, H.; Vant, J.; Turilli, M.; Vermaas, J.; Jha, S.; Singharoy, A.* Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting. J. Chem. Info. Model (Accepted). https://www.biorxiv.org/content/10.1101/2021.12.07.471672v3.full
5. Ray, S.; Berry, S.; Wilson, E.A.; Zhang, C.H.; Shekhar, M.; Singharoy, A.; Gaudet, R. High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter. eLife 2023, 12, e84006.
2022:
6. Shekhar, M.; Gupta, C.; Suzuki, K.; Chan, C.K.; Murata, T. Singharoy, A.* Revealing a hidden intermediate of rotatory catalysis with X-ray crystallography and molecular simulations. ACS Cent. Sci. 2022, 8, 915.
7. Gupta, C.; Sarkar, D. Tieleman, P.; Singharoy, A.* The ugly, bad and good Stories of Large-scale biomolecular simulations. Curr. Opin. Struct. Biol 2022, 73, 102338.
8. Mashayekhi, G.; Vant, J.; Ourmazd, A.; Singharoy, A.* Energy landscape of the SARS-CoV-2 reveals extensive conformational heterogeneity. Curr. Res. Struct. Biol. 2022, 4, 68
9. Kit-Chan, C.; Singharoy, A.; Tajkhorshid, E.“Anionic Lipids Confine Cytochrome c2 to the Surface of Bioenergetic Membranes without Compromising Its Interaction with Redox Partners” Biochemistry 2022, 61, 385.
10. Vant, J.; Sarkar, D.; Vermaas, J.; Singharoy, A.* Exploring cryo-electron microscopy with molecular dynamics. Biochemical Soc. Trans. 2022, 50, 569.
2021:
11. Baker, A. et al, Singharoy, A.*; Borad, B.* The Structure of ChAdOx1/AZD-1222 reveals interactions with CAR and PF4 with implications for vaccine-induced immune thrombotic thrombocytopenia. Science. Adv. 2021, 7, eabl8213.
12. Shekhar, M.; Terashi, G.; Gupta, C.; Debussche, G.; Sisco, N; Nguyen, J.;Zook, J.; Vant, J.; Sarkar, D.; Fromme, P.; Van Horn, W.D.; Tajkhorshid, E.; Kihara, D.; Dill, K.; Perez, A., Singharoy, A*. CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics. Matter. 2021, 4, 3195 (Cover article).
13. Lukas, T.; Gupta, C.; Altman, M.O.; Sanchez, E., Naticchia, M. R.; Gagneux, P.; Singharoy, A.; Godula, K. Mucin-mimetic glycan arrays integrating machine learning for analyzing receptor pattern recognition by influenza A viruses. Chem 2021, 7, 3393.
14. Wilson, E.; Hirnease, G.; Anderson, K.A.; Singharoy, A.* Total predicted MHC-I epitope load is inversely associated with population mortality from SARS-CoV-2. Cell Rep. Med. 2021, 2, 100221.
2020:
15. Gupta, C.; Khaniya, U.; Chan, C.K.; Dehez, F.; Shekhar, M.; Gunner, M. R.; Sazanov, L.; Chipot, C.; Singharoy, A.* Charge transfer and chemo-mechanical coupling in respiratory complex I. J. Am. Chem. Soc. 2020, 142, 9220.
16. Khaniya, U.; Gupta, C.; Cai, X.; Mao, J.; Kaur, D.; Zhang, Y.; Singharoy, A. Gunner, M. R. Hydrogen bond network analysis reveals the pathway for the proton transfer in the E-channel of T. thermophilus Complex I. BBA Bioenerg. 2020, 1861, 148240.
17. Vant, J.; Sarkar. D.; Streitweiser, E.; Fiorin, G.; Skeel, R.; Singharoy. A*. Data-guided Multi-Map variables for ensemble refinement of molecular movies. J Chem. Phys. 2020, 153, 214102.
18. Mittal, S.; Vant, J. W.; Shekhar, M. S.; Rowely, C.; Singharoy, A.*, Flexible fitting of small-molecules into electron microscopy maps using molecular dynamics simulations with Neural Network Potentials. J. Chem. Info. Model. 2020, 60, 2591.
19. Dashti, A.; Shekhar, M. S.; Hail, D; Ben, Mashayekhi; G., Schwander, P.; Georges, A. des*; Frank, J.*; Singharoy, A.*; Ourmazd, A.* Functional pathways of biomolecules retrieved from single-particle snapshots. Nature Comm. 2020, 11, 4734.
20. Roh, S-H.; Shekhar, M.; Pintilie, G.; Chipot, C.; Wilkens, S*; Singharoy, A.*; Chiu. W.* CryoEM and MD infer water-mediated proton transport and autoinhibition mechanisms of Vo complex. Science. Adv. 2020, 6, eabb9605.
21. Zook, J et al. Singharoy, A.*; Fromme, P*. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure 2020, 28, 1.
2019:
22. Singharoy, A.*; Maffeo, C; Delgado-Magnero, K.H.; Swainsbury, D. J. K; Sener, M; Kleinekathöfer, U.; Isralewitz, B.; Teo, I.; Chandler, D.; Vant, J. W.; Stone, J. E.; Phillips, J.; Pogorelov, T.V.; Mallus, M. I.; Chipot, C.; Luthey-Schulten, Z.; Tieleman, P.; Hunter, C. N.; Tajkhorshid, E.; Aksimentiev, A.; Schulten, K. Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell 2019, 179, 1098.
23. Singharoy, A.*; Chipot, C.; Ekimoto, T.; Suzuki, K.; Ikeguchi, M.; Yamato, I.; Murata, T. Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses. Front. Physiol. 2019, 10, 46.
2018:
24. Benson, C. R.; Maffeo, C.; Fatila, E. M.; Liu, Y.; Sheetz, E. G.; Aksimentiev, A.; Singharoy, A.*; Flood, A. H.* Inchworm Movement of Two Rings Switching onto a thread by biased Brownian diffusion represent a Three-body problem. Proc. Nat. Acad. Sci. 2018, 115, 9391.

From University of Illinois at Urbana Champaign– postdoctoral studies

2017:
25. Singharoy, A; Chipot, C.; Moradi, M.; Schulten, K. Chemomechanical coupling in hexameric protein-protein interfaces harness energy within V- type ATPases. J. Am. Chem. Soc. 2017, 139, 293.
26. Singharoy, A.; Chipot, C. Methodology for the simulation of molecular motors at different scales. J. Phys. Chem. B 2017, 121, 3502.
27. Qi, Y.; Lee, J.; Singharoy, A.; McGreevy, R.; Schulten, K.; Im, W. CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments. J. Phys. Chem. B 2017, 121, 3718.
28. McGreevy, R.; Singharoy, A.; Schulten, K. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. Methods 2017, 17, 50.
2016:
29. Singharoy, A.; Liu, Y.; Mayne, C.; Sengupta, A.; Raghavachari, A.; Schulten, K.; Flood, A. Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles. J. Am. Chem. Soc. 2016, 138, 4843. 42.
30. Singharoy, A.; Teo, I.; Mcgreevy, R.; Stone, J.; Jhao, J.; Schulten, K. Molecular Dynamics-based Refinement and Validation with Resolution Exchange MDFF for sub-5 Å Cryo-Electron Microscopy Maps. eLife 2016, 5, e16105.
31. Bozzi, A. T.; Bane, L.; Weihofen, W.; McCabe, A.; Singharoy, A.; Chipot, C.; Schulten, K.; Gaudet, R. Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters. Proc. Nat. Acad. Sci. 2016, 113, 10310.
32. Sener, M.; Strumpher, J.; Singharoy, A.; Hunter, N.; Schulten, K. Overall energy conversion efficiency of a photosynthetic vesicle eLife 2016, 5, e09541. 43.
33. Goh, B.; Hadden, J.; Bernardi, R.; Singharoy, A.; McGreevy, R.; Rudack, T.; Cassidy, K.; Schulten, K. “Computational methodologies for real-space structural refinement of large macromolecular complexes” Ann. Rev. Biophys. 2016, 45, 253.
2015:
Singharoy, A.; Venkatakrishnan, B.; Liu, Y.; Mayne, C. G.; Lee, S.; Chen, C. H.; Zlotnick, A.; Schulten, K.; Flood, A. H. Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles. J. Am. Chem. Soc. 2015, 137, 8810.
2014:
Mcgreevy, R.; Singharoy, A.; Li, Q.; Zhang, J.; Xu, D.; Perozo, E.; Schulten, K. xMDFF: Molecular dynamics flexible fitting of low-resolution X-Ray structures. Acta. Cryst. D 2014, 70, 2344.
36. Wickles, S.; Singharoy, A.; Andreani, J.; Seemayer, S.; Bischoff, L.; Berninghausen, O.; Soeding, J.; Schulten, K.; Van der Sluis, E. O.; Beckmann, R. A Structural Model of the Active Ribosome-bound Membrane Protein Insertase YidC. eLife 2014, 3, e03035.
37. Li, Q.; Wanderling, S.; Paduch, M.; Medovoy, D.; Singharoy, A.; Mcgreevy, R.; Villalba-Galea, C.; Hulse, R.E.; Roux, B.; Schulten, K.; Kossaikoff, A.; Perozo, E. Structural mechanism of Voltage-dependent Gating in an Isolated Voltage-sensing Domain. Nat. Struct. Mol. Biol. 2014, 21, 244.
38. Yang, J; Singharoy, A.; Sereda, Y. V.; Ortoleva, P. J. Quasiequivalence of Multiscale Coevolution and Ensemble MD Simulations: A Demonstration with Lactoferrin. Chem. Phys. Lett. 2014, 616, 154.

From Indiana University– doctoral studies

2013:
39. Singharoy, A.; Polavarapu, A.; Joshi, H.; Baik, M.; Ortoleva, P. J. Epitope Fluctuation in the Human Papillomavirus are under Dynamic Allosteric Control: A Computational Evaluation of a New Vaccine Design Strategy. J. Am. Chem. Soc. 2013, 135, 18458.
40. Joshi, H.; Lewis, K.; Singharoy, A.; Ortoleva, P.J. Epitope Engineering and Molecular Metrics of Immunogenicity: A Computational Approach to VLP-based Vaccine Design Vaccine 2013, 31, 4841.
41. Quick, R. A.; Singharoy, A.; Ortoleva, P. J. Quasiperiodic Oscillation and Possible Second Law Violation in a Nanosystem Chem. Phys. Lett. 2013, 571, 61. 38.
Pankavich, S.; Singharoy, A.; Ortoleva, P.J. Hierarchical Multiscale Modeling of Macromolecules and their Assemblies. Soft Matter 2013, 9, 4319.
2012:
43. Singharoy, A.; Joshi, H.; Ortoleva, P.J.; Miao, Y. Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of Bionanosystems. J. Phys. Chem. B 2012, 116, 8423.
44. Singharoy, A.; Joshi, H. J.; Ortoleva, P. J. Multiscale Macromolecular Simulation: Role of Evolving Ensembles. J. Chem. Info. Model. 2012, 52, 2638.
45. Singharoy, A.; Sereda, Y.; Ortoleva, P. J. Hierarchical Order Parameters for Macromolecular Assembly Simulation I: Construction and Dynamical Properties of Order Parameters. J. Chem. Theor. Comput. 2012, 8, 1379. 17.
46. Sereda, Y.; Singharoy, A.; Jarrold, M. F.; Ortoleva, P. J. An Information Theory Approach to Multiple Free-energy Basin Discovery. J. Phys. Chem. B 2012, 116, 8534. 18.
2011:
47. Singharoy, A.; Cheluvaraja, S.; Ortoleva, P. J. Order Parameters for Macromolecules: Application to Multiscale Simulation. J. Chem. Phys. 2011, 134, 044104 (Reviewed in Virtual Journals in Science and Technology).
2010:
48. Singharoy, A.; Yesnik, A.; Ortoleva, P. J. Multiscale Analytic Continuation Approach to Nanosystem Simulation: Applications to Virus Electrostatics J.Chem. Phys. 2010, 132, 174112 (Reviewed in Virtual Journals in Science and Technology).
2007:
49. Ali, Md. E.; Singharoy, A.; Datta, S.N. Molecular Tailoring and Prediction of Strongly Ferromagnetically Coupled Trimethylenemethane-Based Nitroxide Diradicals. J. Phys. Chem. A 2007, 111, 5523.
Book Chapters
50. Wilson, E.; Vant, J.; Layton, J.; Boyd, R.; Lee, H.; Turilli, M.; Hernandez, B.; Wilkinson, S.; Jha, S.; Gupta, C.; Sarkar, D.; and Singharoy, A. All You Want to Know About Large System Simulations, Methods in Molecular Biology. Method Mol. Biol. 2022 (Accepted, pending publication).
51. Gupta, G.; Khaniya, U.; Vant, J.; Shekhar, M.; Mao, J.; Gunner, M.R.; Singharoy, A. Poor Person’s pH Simulation of Membrane Proteins. Method Mol. Biol. 2021.
52. ‡Vant, J.W.; Sarkar, D.; Gupta, C.; Shekhar, M. S.; Mittal, S.; Singharoy, A.*, MDFF All You Wanted to Know About Resolution Exchange. Method Mol. Biol. 2019 Elsevier Publications.
53. Singharoy, A.; Joshi, H.; Cheluvaraja, S.; Brown, D.; Ortoleva, P. J. “Simulating Microbial Systems: Addressing Model Uncertainty/Incompleteness via Multiscaling and Entropy Methods” Microbial System Biology: Methods and Protocols, Editor: A. Navid, Springer Science: New York, 2012.
54. Joshi, H.; Singharoy, A.; Sereda, Y.; Cheluvaraja, S.; Ortoleva, P. J. “Multiscale Simulation of Microbe Structure and Dynamics” Prog. Biophys. Mol. Biol. 2011, 107, 200.