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Abhishek Singharoy, Ph.D. - Publications

Affiliations: 
2012 Chemistry Indiana University, Bloomington, Bloomington, IN, United States 
Area:
systems biology, physical chemistry
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51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Gupta C, Sarkar D, Tieleman DP, Singharoy A. The ugly, bad, and good stories of large-scale biomolecular simulations. Current Opinion in Structural Biology. 73: 102338. PMID 35245737 DOI: 10.1016/j.sbi.2022.102338  0.303
2021 Wilson E, Vant J, Layton J, Boyd R, Lee H, Turilli M, Hernández B, Wilkinson S, Jha S, Gupta C, Sarkar D, Singharoy A. Large-Scale Molecular Dynamics Simulations of Cellular Compartments. Methods in Molecular Biology (Clifton, N.J.). 2302: 335-356. PMID 33877636 DOI: 10.1007/978-1-0716-1394-8_18  0.356
2020 Vant JW, Sarkar D, Streitwieser E, Fiorin G, Skeel R, Vermaas JV, Singharoy A. Data-guided Multi-Map variables for ensemble refinement of molecular movies. The Journal of Chemical Physics. 153: 214102. PMID 33291927 DOI: 10.1063/5.0022433  0.324
2020 Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A. Retrieving functional pathways of biomolecules from single-particle snapshots. Nature Communications. 11: 4734. PMID 32948759 DOI: 10.1038/S41467-020-18403-X  0.339
2020 Phillips JC, Hardy DJ, Maia JDC, Stone JE, Ribeiro JV, Bernardi RC, Buch R, Fiorin G, Hénin J, Jiang W, McGreevy R, Melo MCR, Radak BK, Skeel RD, Singharoy A, et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153: 044130. PMID 32752662 DOI: 10.1063/5.0014475  0.429
2020 Vant JW, Sarkar D, Gupta C, Shekhar MS, Mittal S, Singharoy A. Molecular Dynamics Flexible Fitting: All You Want to Know About Resolution Exchange. Methods in Molecular Biology (Clifton, N.J.). 2165: 301-315. PMID 32621233 DOI: 10.1007/978-1-0716-0708-4_18  0.389
2020 Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov L, Chipot C, Singharoy A. Charge transfer and chemo-mechanical coupling in respiratory complex I. Journal of the American Chemical Society. PMID 32347721 DOI: 10.1021/Jacs.9B13450  0.35
2020 Vant J, Lahey SJ, Jana K, Shekhar M, Sarkar D, Munk BH, Kleinekathöfer U, Mittal S, Rowley CN, Singharoy A. Flexible fitting of small-molecules into electron microscopy maps using molecular dynamics simulations with Neural Network Potentials. Journal of Chemical Information and Modeling. PMID 32207947 DOI: 10.1021/Acs.Jcim.9B01167  0.374
2020 Zook J, Shekhar M, Hansen D, Conrad C, Grant T, Gupta C, White T, Barty A, Basu S, Zhao Y, Zatsepin N, Ishchenko A, Batyuk A, Gati C, Li C, ... ... Singharoy A, et al. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure (London, England : 1993). PMID 32142641 DOI: 10.1016/J.Str.2020.02.005  0.322
2020 Salas-Estrada LA, Grant TD, Perera SM, Struts AV, Chawla U, Xu X, Fried SD, Weerasinghe N, Mendez D, Alvarez R, Karpos K, Lisova S, Zaare S, Nazari R, Zatsepsin N, ... Singharoy A, et al. Rhodopsin's Ultra-Fast Activation Dynamics in Bilayer and Micelle Environments Biophysical Journal. 118: 92a. DOI: 10.1016/J.Bpj.2019.11.669  0.319
2020 Layton J, Nagaratnam N, Jernigan RJ, Schneider J, Flint A, Mroczkowski B, Fromme P, Garcia JM, Singharoy A. Molecular Dynamics Simulations for Improving Crystal Quality and Illuminating the Function of Taspase1: A Therapeutic Target Biophysical Journal. 118: 507a. DOI: 10.1016/J.Bpj.2019.11.2794  0.332
2020 Wilson EA, Anderson K, Singharoy A. Resolving the Connection between Major Histocompatibilty Complexes and Immune Outcomes using Unsupervised Clustering of Molecular Dynamics Simulations Biophysical Journal. 118: 452a. DOI: 10.1016/J.Bpj.2019.11.2521  0.329
2020 Doole FT, Kit Chan C, Kim M, Singharoy A, Brown MF. Antimicrobial Peptide Functionalized Biomaterials Investigated by Molecular Dynamics Simulations Biophysical Journal. 118: 380a-381a. DOI: 10.1016/J.Bpj.2019.11.2173  0.346
2019 Singharoy A, Maffeo C, Delgado-Magnero KH, Swainsbury DJK, Sener M, Kleinekathöfer U, Vant JW, Nguyen J, Hitchcock A, Isralewitz B, Teo I, Chandler DE, Stone JE, Phillips JC, Pogorelov TV, et al. Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell. 179: 1098-1111.e23. PMID 31730852 DOI: 10.1016/J.Cell.2019.10.021  0.428
2019 Perez A, Shekhar M, Terashi G, Kihara D, Dill KA, Tajkhorshid E, Singharoy A. MAINMAST-MELD-MDFF: Denovo Structure-Determination with Data-Guided Molecular Dynamics Biophysical Journal. 116: 287a-288a. DOI: 10.1016/J.Bpj.2018.11.1553  0.378
2019 Salas L, Mendez D, Meza-Aguilar JD, Perera SM, Singharoy A, Struts AV, Zatsepin NA, Kirian RA, Grant TD, Fromme P, Brown MF, Grossfield A. Study of Ultra-Fast Rhodopsin Activation Dynamics with Molecular Dynamics Simulations Biophysical Journal. 116: 205a. DOI: 10.1016/J.Bpj.2018.11.1131  0.408
2018 Wang Y, Shekhar M, Thifault D, Williams CJ, Mcgreevy R, Richardson J, Singharoy A, Tajkhorshid E. Constructing Atomic Structural Models into Cryo-EM Densities using Molecular Dynamics - Pros and Cons. Journal of Structural Biology. PMID 30092279 DOI: 10.1016/J.Jsb.2018.08.003  0.384
2018 Benson CR, Maffeo C, Fatila EM, Liu Y, Sheetz EG, Aksimentiev A, Singharoy A, Flood AH. Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem. Proceedings of the National Academy of Sciences of the United States of America. PMID 29735677 DOI: 10.1073/Pnas.1719539115  0.32
2017 Singharoy A, Chipot C. Methodology for the Simulation of Molecular Motors at Different Scales. The Journal of Physical Chemistry. B. 121: 3502-3514. PMID 28423900 DOI: 10.1021/Acs.Jpcb.6B09350  0.371
2017 Singharoy A, Schulten K. Atom-Resolved View of a Cell Organelle on a Computational Microscope Biophysical Journal. 112: 176a. DOI: 10.1016/J.Bpj.2016.11.973  0.399
2016 Qi Y, Lee J, Singharoy A, Mcgreevy R, Schulten K, Im W. CHRAMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments. The Journal of Physical Chemistry. B. PMID 27936734 DOI: 10.1021/Acs.Jpcb.6B10568  0.446
2016 Singharoy A, Chipot C, Moradi M, Schulten K. Chemomechanical coupling in hexameric protein-protein interfaces harness energy within V-type ATPases. Journal of the American Chemical Society. PMID 27936329 DOI: 10.1021/Jacs.6B10744  0.333
2016 Singharoy A, Barragan AM, Thangapandian S, Tajkhorshid E, Schulten K. Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2. Journal of the American Chemical Society. PMID 27508459 DOI: 10.1021/Jacs.6B01193  0.35
2016 Singharoy A, Teo I, McGreevy R, Stone JE, Zhao J, Schulten K. Molecular dynamics-based renement and validation with Resolution Exchange MDFF for sub-5 Å cryo-electron microscopy maps. Elife. 5. PMID 27383269 DOI: 10.7554/Elife.16105  0.366
2016 Goh BC, Hadden JA, Bernardi RC, Singharoy A, McGreevy R, Rudack T, Cassidy CK, Schulten K. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Annual Review of Biophysics. PMID 27145875 DOI: 10.1146/Annurev-Biophys-062215-011113  0.36
2016 Liu Y, Singharoy A, Mayne CG, Sengupta A, Raghavachari K, Schulten K, Flood AH. Flexibility Coexists with Shape-persistence in Cyanostar Macrocycles. Journal of the American Chemical Society. PMID 27014837 DOI: 10.1021/Jacs.6B00712  0.332
2016 McGreevy R, Teo I, Singharoy A, Schulten K. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. Methods (San Diego, Calif.). PMID 26804562 DOI: 10.1016/J.Ymeth.2016.01.009  0.423
2016 Singharoy A, Teo I, McGreevy R, Stone JE, Zhao J, Schulten K. Author response: Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps Elife. DOI: 10.7554/Elife.16105.057  0.307
2016 Radak BK, Singharoy A, Schulten K, Roux B. Inclusion of ph Effects in Molecular Dynamics Simulations of Membranes and Membrane Proteins Biophysical Journal. 110: 646a. DOI: 10.1016/J.Bpj.2015.11.3456  0.401
2015 Singharoy A, Venkatakrishnan B, Liu Y, Mayne CG, Lee S, Chen CH, Zlotnick A, Schulten K, Flood AH. Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles. Journal of the American Chemical Society. 137: 8810-8. PMID 26121416 DOI: 10.1021/Jacs.5B04407  0.373
2015 Singharoy A, Chandler D, Durrant J, Sener M, Amaro R, Schulten K. The Do's and Do Not's of a 100 Million Atom Molecular Dynamics Simulation Biophysical Journal. 108: 158a. DOI: 10.1016/J.Bpj.2014.11.872  0.451
2015 Barragan AM, Singharoy A, Crofts AR, Schulten K, Solov’yov IA. New Perspectives on Quinol Binding Motifs at the bc1 Complex Based on MD Simulations Biophysical Journal. 108: 602a-603a. DOI: 10.1016/J.Bpj.2014.11.3281  0.327
2015 Singharoy A, Wickles S, Beckmann R, Schulten K. A Structural Model of the Ribosome-Bound Protein Insertase YidC Reveals Lateral Translocation of the Nascent Chain Biophysical Journal. 108: 390a. DOI: 10.1016/J.Bpj.2014.11.2138  0.317
2015 Singharoy A, Schulten K. Towards the Simulation of a Complete ATP Synthase: Unravelling the Structural Basis of the Enzyme's Reversible Action Biophysical Journal. 108: 319a. DOI: 10.1016/J.Bpj.2014.11.1736  0.337
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 Crystallographica. Section D, Biological Crystallography. 70: 2344-55. PMID 25195748 DOI: 10.1107/S1399004714013856  0.397
2014 Yang J, Singharoy A, Sereda YV, Ortoleva PJ. Quasiequivalence of multiscale coevolution and ensemble MD simulations: A demonstration with lactoferrin Chemical Physics Letters. 616: 154-160. DOI: 10.1016/J.Cplett.2014.10.020  0.609
2013 Singharoy A, Polavarapu A, Joshi H, Baik MH, Ortoleva P. Epitope fluctuations in the human papillomavirus are under dynamic allosteric control: a computational evaluation of a new vaccine design strategy. Journal of the American Chemical Society. 135: 18458-68. PMID 24199651 DOI: 10.1021/Ja407489R  0.574
2013 Joshi H, Lewis K, Singharoy A, Ortoleva PJ. Epitope engineering and molecular metrics of immunogenicity: A computational approach to VLP-based vaccine design Vaccine. 31: 4841-4847. PMID 23933338 DOI: 10.1016/J.Vaccine.2013.07.075  0.505
2013 Ortoleva P, Singharoy A, Pankavich S. Hierarchical Multiscale Modeling of Macromolecules and their Assemblies. Soft Matter. 9: 4319-4335. PMID 23671457 DOI: 10.1039/C3Sm50176K  0.641
2013 Quick R, Singharoy A, Ortoleva P. Quasiperiodic oscillation and possible Second Law violation in a nanosystem Chemical Physics Letters. 571: 61-65. DOI: 10.1016/J.Cplett.2013.03.083  0.543
2012 Singharoy A, Joshi H, Ortoleva PJ. Multiscale macromolecular simulation: Role of evolving ensembles Journal of Chemical Information and Modeling. 52: 2638-2649. PMID 22978601 DOI: 10.1021/Ci3002952  0.623
2012 Singharoy A, Sereda Y, Ortoleva PJ. Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters. Journal of Chemical Theory and Computation. 8: 1379-1392. PMID 22661911 DOI: 10.1021/Ct200574X  0.652
2012 Singharoy A, Joshi H, Cheluvaraja S, Miao Y, Brown D, Ortoleva P. Simulating microbial systems: addressing model uncertainty/incompleteness via multiscale and entropy methods. Methods in Molecular Biology (Clifton, N.J.). 881: 433-67. PMID 22639222 DOI: 10.1007/978-1-61779-827-6_15  0.65
2012 Sereda YV, Singharoy AB, Jarrold MF, Ortoleva PJ. Discovering free energy basins for macromolecular systems via guided multiscale simulation. The Journal of Physical Chemistry. B. 116: 8534-44. PMID 22423635 DOI: 10.1021/Jp2126174  0.533
2012 Singharoy A, Joshi H, Miao Y, Ortoleva PJ. Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies. The Journal of Physical Chemistry. B. 116: 8423-34. PMID 22356532 DOI: 10.1021/Jp2119247  0.685
2012 Singharoy A, Joshi H, Miao Y, Ortoleva PJ. Space warping order parameters and symmetry: Application to multiscale simulation of macromolecular assemblies Journal of Physical Chemistry B. 116: 8423-8434. DOI: 10.1021/jp2119247  0.61
2012 Singharoy A, Sereda Y, Ortoleva PJ. Hierarchical order parameters for macromolecular assembly simulations. 1. Construction and dynamical properties of order parameters Journal of Chemical Theory and Computation. 8: 1379-1392. DOI: 10.1021/ct200574x  0.533
2011 Joshi H, Singharoy A, Sereda YV, Cheluvaraja SC, Ortoleva PJ. Multiscale simulation of microbe structure and dynamics Progress in Biophysics and Molecular Biology. 107: 200-217. PMID 21802438 DOI: 10.1016/J.Pbiomolbio.2011.07.006  0.636
2011 Singharoy A, Cheluvaraja S, Ortoleva P. Order parameters for macromolecules: application to multiscale simulation. The Journal of Chemical Physics. 134: 044104. PMID 21280684 DOI: 10.1063/1.3524532  0.622
2011 Singharoy A, Ortoleva P. Order Parameters for Multiscale Simulation of Bio-Nanosystems Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.2389  0.642
2010 Singharoy A, Yesnik AM, Ortoleva P. Multiscale analytic continuation approach to nanosystem simulation: applications to virus electrostatics. The Journal of Chemical Physics. 132: 174112. PMID 20459161 DOI: 10.1063/1.3424771  0.555
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