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Items: 31

1.

Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses.

Singharoy A, Chipot C, Ekimoto T, Suzuki K, Ikeguchi M, Yamato I, Murata T.

Front Physiol. 2019 Feb 5;10:46. doi: 10.3389/fphys.2019.00046. eCollection 2019. Review.

2.

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

Wang Y, Shekhar M, Thifault D, Williams CJ, McGreevy R, Richardson J, Singharoy A, Tajkhorshid E.

J Struct Biol. 2018 Nov;204(2):319-328. doi: 10.1016/j.jsb.2018.08.003. Epub 2018 Aug 7.

PMID:
30092279
3.

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

Benson CR, Maffeo C, Fatila EM, Liu Y, Sheetz EG, Aksimentiev A, Singharoy A, Flood AH.

Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):9391-9396. doi: 10.1073/pnas.1719539115. Epub 2018 May 7.

4.

Methodology for the Simulation of Molecular Motors at Different Scales.

Singharoy A, Chipot C.

J Phys Chem B. 2017 Apr 20;121(15):3502-3514. doi: 10.1021/acs.jpcb.6b09350. Epub 2016 Nov 30.

5.

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.

J Phys Chem B. 2017 Apr 20;121(15):3718-3723. doi: 10.1021/acs.jpcb.6b10568. Epub 2016 Dec 23.

6.

Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.

Singharoy A, Chipot C, Moradi M, Schulten K.

J Am Chem Soc. 2017 Jan 11;139(1):293-310. doi: 10.1021/jacs.6b10744. Epub 2016 Dec 23.

7.

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

Bozzi AT, Bane LB, Weihofen WA, Singharoy A, Guillen ER, Ploegh HL, Schulten K, Gaudet R.

Structure. 2016 Dec 6;24(12):2102-2114. doi: 10.1016/j.str.2016.09.017. Epub 2016 Nov 10.

8.

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

Bozzi AT, Bane LB, Weihofen WA, McCabe AL, Singharoy A, Chipot CJ, Schulten K, Gaudet R.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10310-5. doi: 10.1073/pnas.1607734113. Epub 2016 Aug 29.

9.

Overall energy conversion efficiency of a photosynthetic vesicle.

Sener M, Strumpfer J, Singharoy A, Hunter CN, Schulten K.

Elife. 2016 Aug 26;5. pii: e09541. doi: 10.7554/eLife.09541.

10.

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

Singharoy A, Barragan AM, Thangapandian S, Tajkhorshid E, Schulten K.

J Am Chem Soc. 2016 Sep 21;138(37):12077-89. doi: 10.1021/jacs.6b01193. Epub 2016 Sep 7.

11.

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

Singharoy A, Teo I, McGreevy R, Stone JE, Zhao J, Schulten K.

Elife. 2016 Jul 7;5. pii: e16105. doi: 10.7554/eLife.16105.

12.

Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing.

Stone JE, Sener M, Vandivort KL, Barragan A, Singharoy A, Teo I, Ribeiro JV, Isralewitz B, Liu B, Goh BC, Phillips JC, MacGregor-Chatwin C, Johnson MP, Kourkoutis LF, Hunter CN, Schulten K.

Parallel Comput. 2016 Jul;55:17-27.

13.

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

Goh BC, Hadden JA, Bernardi RC, Singharoy A, McGreevy R, Rudack T, Cassidy CK, Schulten K.

Annu Rev Biophys. 2016 Jul 5;45:253-78. doi: 10.1146/annurev-biophys-062215-011113. Epub 2016 May 2. Review.

14.

Flexibility Coexists with Shape-Persistence in Cyanostar Macrocycles.

Liu Y, Singharoy A, Mayne CG, Sengupta A, Raghavachari K, Schulten K, Flood AH.

J Am Chem Soc. 2016 Apr 13;138(14):4843-4851. doi: 10.1021/jacs.6b00712. Epub 2016 Apr 5.

15.

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

McGreevy R, Teo I, Singharoy A, Schulten K.

Methods. 2016 May 1;100:50-60. doi: 10.1016/j.ymeth.2016.01.009. Epub 2016 Jan 21.

16.

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

Singharoy A, Venkatakrishnan B, Liu Y, Mayne CG, Lee S, Chen CH, Zlotnick A, Schulten K, Flood AH.

J Am Chem Soc. 2015 Jul 15;137(27):8810-8. doi: 10.1021/jacs.5b04407. Epub 2015 Jun 29.

17.

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.

Acta Crystallogr D Biol Crystallogr. 2014 Sep;70(Pt 9):2344-55. doi: 10.1107/S1399004714013856. Epub 2014 Aug 29.

18.

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 EO, Beckmann R.

Elife. 2014 Jul 10;3:e03035. doi: 10.7554/eLife.03035.

19.

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 CA, Hulse RE, Roux B, Schulten K, Kossiakoff A, Perozo E.

Nat Struct Mol Biol. 2014 Mar;21(3):244-52. doi: 10.1038/nsmb.2768. Epub 2014 Feb 2.

20.

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 MH, Ortoleva P.

J Am Chem Soc. 2013 Dec 11;135(49):18458-68. doi: 10.1021/ja407489r. Epub 2013 Nov 25.

PMID:
24199651
21.

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

Joshi H, Lewis K, Singharoy A, Ortoleva PJ.

Vaccine. 2013 Oct 1;31(42):4841-7. doi: 10.1016/j.vaccine.2013.07.075. Epub 2013 Aug 9.

PMID:
23933338
22.

Hierarchical Multiscale Modeling of Macromolecules and their Assemblies.

Ortoleva P, Singharoy A, Pankavich S.

Soft Matter. 2013 Apr 28;9(16):4319-4335.

23.

Multiscale macromolecular simulation: role of evolving ensembles.

Singharoy A, Joshi H, Ortoleva PJ.

J Chem Inf Model. 2012 Oct 22;52(10):2638-49. doi: 10.1021/ci3002952. Epub 2012 Sep 28.

24.

Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters.

Singharoy A, Sereda Y, Ortoleva PJ.

J Chem Theory Comput. 2012 Apr 10;8(4):1379-1392. Epub 2012 Mar 13.

25.

Simulating microbial systems: addressing model uncertainty/incompleteness via multiscale and entropy methods.

Singharoy A, Joshi H, Cheluvaraja S, Miao Y, Brown D, Ortoleva P.

Methods Mol Biol. 2012;881:433-67. doi: 10.1007/978-1-61779-827-6_15.

PMID:
22639222
26.

Discovering free energy basins for macromolecular systems via guided multiscale simulation.

Sereda YV, Singharoy AB, Jarrold MF, Ortoleva PJ.

J Phys Chem B. 2012 Jul 26;116(29):8534-44. doi: 10.1021/jp2126174. Epub 2012 Mar 30.

27.

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

Singharoy A, Joshi H, Miao Y, Ortoleva PJ.

J Phys Chem B. 2012 Jul 26;116(29):8423-34. doi: 10.1021/jp2119247. Epub 2012 Mar 9.

28.

Multiscale simulation of microbe structure and dynamics.

Joshi H, Singharoy A, Sereda YV, Cheluvaraja SC, Ortoleva PJ.

Prog Biophys Mol Biol. 2011 Oct;107(1):200-17. doi: 10.1016/j.pbiomolbio.2011.07.006. Epub 2011 Jul 23.

29.

Order parameters for macromolecules: application to multiscale simulation.

Singharoy A, Cheluvaraja S, Ortoleva P.

J Chem Phys. 2011 Jan 28;134(4):044104. doi: 10.1063/1.3524532.

30.

Multiscale analytic continuation approach to nanosystem simulation: applications to virus electrostatics.

Singharoy A, Yesnik AM, Ortoleva P.

J Chem Phys. 2010 May 7;132(17):174112. doi: 10.1063/1.3424771.

31.

Azithromycin in the treatment of cholera in children.

Bhattacharya MK, Dutta D, Ramamurthy T, Sarkar D, Singharoy A, Bhattacharya SK.

Acta Paediatr. 2003 Jun;92(6):676-8.

PMID:
12856976

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