Journal Articles
2023-2024
64. Lev Levintov and Harish Vashisth
Adenine methylation enhances the conformational flexibility of an RNA hairpin tetraloop
J. Phys. Chem. B 128:3157-3166 (2024) PDF
63. Jyoti Verma and Harish Vashisth
Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases
Proteins doi: 10.1002/prot.26685 (2024) PDF
62. Amit Kumar and Harish Vashisth
Quantitative assessment of energetic contributions of residues in a SARS-CoV-2 viral-enzyme/nanobody interface
J. Chem. Inf. Model. 64:2068-2076 (2024) PDF
61. Son Nguyen, Lev Levintov, Roy P Planalp, and Harish Vashisth
Interactions and transport of a bioconjugated peptide targeting the mitomembrane
Bioconjugate Chem. 35:371-380 (2024) PDF
60. Brunno C. Rocha and Harish Vashisth
Porous self-assemblies mediated by dumbbell particles as cross-linking agents
J. Chem. Theory Comput. 20:1590-1599 (2024) PDF
59. Remya Ann Mathews Kalapurakal, Brunno C. Rocha, and Harish Vashisth
Self-assembly in an experimentally realistic model of lobed patchy colloids
ACS App. Bio Mater. 7:535-542 (2024) PDF
58. Lev Levintov and Harish Vashisth
Structural and computational studies of HIV-1 RNA
RNA Biol. 21:1-32 (2024) PDF
57. Amit Kumar and Harish Vashisth
Mechanism of ligand discrimination by the NMT1 riboswitch
J. Chem. Inf. Model. 63:4864-4874 (2023) PDF
56. Shubhandra Tripathi, Rick H. Cote, and Harish Vashisth
Coupling of conformational dynamics and inhibitor binding in the phosphodiesterase-5 family
Protein Sci. 32:e4720 (2023) PDF
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55. Saikat Pal, Amit Kumar, and Harish Vashisth
Role of dynamics and mutations in interactions of a zinc finger antiviral protein with CG-rich viral RNA
J. Chem. Inf. Model. 63:1002-1011 (2023) PDF
54. Biswajit Gorai and Harish Vashisth
Structural models of viral insulin-like peptides and their analogs
Proteins 91:62-73 (2023) PDF
2018-2022
53. R. Stolz, A. Kolln, B. Rocha, A. Brinks, A. Eagleton, L. Mendecki, Harish Vashisth, and Katherine Mirica
Epitaxial self-Assembly of interfaces of 2D Metal–Organic Frameworks for electroanalytical detection of neurotransmitters
ACS Nano 16:13869-13883 (2022) PDF
52. Amit Kumar and Harish Vashisth
Role of mutations in differential recognition of viral RNA molecules by peptides
J. Chem. Inf. Model. 62:3381-3390 (2022) PDF
51. Arpita Srivastava, Brunno C. Rocha, and Harish Vashisth
Self-assembly in mixtures of charged lobed particles
Front. Phys. 10:936385 (2022) PDF
50. Jacob Andrzejczyk, Katarina Jovic, Logan M. Brown, Valerie G. Pascetta, Krisztina Varga, and Harish Vashisth
Molecular interactions and inhibition of the SARS-CoV-2 Main Protease by a Thiadiazolidinone derivative
Proteins 90:1896-1907 (2022) PDF
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49. Biswajit Gorai and Harish Vashisth
Progress in simulation studies of insulin structure and function
Front. Endocrinol. 13:908724 (2022) PDF
48. Biswajit Gorai and Harish Vashisth
Structures and interactions of insulin-like peptides from cone snail venom
Proteins 90:680-690 (2022) PDF
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47. Amit Kumar and Harish Vashisth
Conformational dynamics and energetics of viral RNA recognition by lab-evolved proteins
Phys. Chem. Chem. Phys. 23:24773-24779 (2021) PDF
46. Lev Levintov and Harish Vashisth
Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides
Biophys. J. 120:5060-5073 (2021) PDF
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45. Daniel Ryan Barden and Harish Vashisth
Water dynamics in a peptide-appended pillar[5]arene artificial channel in lipid and biomimetic membranes
Front. Chem. 9:753635 (2021) PDF
44. Sanjib Paul and Harish Vashisth
Self-assembly of porous structures from a binary mixture of lobed patchy particles
Front. Phys. 9:767623 (2021) PDF
43. Biswajit Gorai, Brunno Carvalho Rocha, and Harish Vashisth
Design of functionalized lobed particles for porous self-assemblies
JOM 73:2413-2422 (2021) PDF
42. H. Feroz, B. Ferlez, H. Oh, H. Mohammadiarani, T. Ren, C. S. Baker, J. P. Gajewski, D. J. Lugar, S. B. Gaudana, P. Butler, J. Hühn,
M. Lamping, W. J. Parak, M. R. Blatt, C. A. Kerfeld, N. Smirnoff, Harish Vashisth, J. H. Golbeck, and Manish Kumar
Liposome-based measurement of light-driven chloride transport kinetics of halorhodopsin
BBA-Biomembranes 1863:183637 (2021) PDF
41. Lev Levintov and Harish Vashisth
Role of conformational heterogeneity in ligand recognition by viral RNA molecules
Phys. Chem. Chem. Phys. 23:11211-11223 (2021) PDF
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40. Brunno Carvalho Rocha, Sanjib Paul, and Harish Vashisth
Enhanced porosity in self-assembled morphologies mediated by charged lobes on patchy particles
J. Phys. Chem. B "Carol K. Hall Festschrift" 125:3208-3215 (2021) PDF
39. Lev Levintov, Sanjib Paul, and Harish Vashisth
Reaction coordinate and thermodynamics of base flipping in RNA
J. Chem. Theory Comput. 17:1914-1921 (2021) PDF
38. Yong Liu and Harish Vashisth
Allosteric pathways originating at cysteine residues in regulators of G-protein signaling proteins
Biophys. J. 120:517-526 (2021) PDF
37. R. Gupta, Y. Liu, H. Wang, C. T. Nordyke, R. Z. Puterbaugh, K. Varga, F. Chu, H. Ke, Harish Vashisth, R. H. Cote
Structural analysis of the regulatory GAF domains of cGMP phosphodiesterase elucidates the allosteric communication pathway
J. Mol. Biol. 432:5765-5783 (2020) PDF
36. Sanjib Paul and Harish Vashisth
Self-assembly behavior of experimentally realizable lobed patchy particles
Soft Matter 16:8101-8107 (2020) PDF
35. Brunno Carvalho Rocha, Sanjib Paul, and Harish Vashisth
Role of Entropy in Colloidal Self-Assembly
Entropy 22:877 (2020) PDF
34. Lev Levintov and Harish Vashisth
Ligand Recognition in Viral RNA Necessitates Rare Conformational Transitions
J. Phys. Chem. Lett. 11:5426-5432 (2020) PDF
33. Shambhavi Tannir, Lev Levintov, Mark A Townley, Brian M. Leonard, Jan Kubelka, Harish Vashisth, Krisztina Varga, Milan Balaz
Functional Nanoassemblies with Mirror-Image Chiroptical Properties Templated by a Single Homochiral DNA Strand
Chem. Mater. 32:2272-2281 (2020) PDF
32. Sanjib Paul and Harish Vashisth
Self-assembly of lobed particles into amorphous and crystalline porous structures
Soft Matter 16:1142-1147 (2020) PDF
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31. Vincent S. Shaw, Mohammadjavad Mohammadi, Josiah A. Quinn, Harish Vashisth, and Richard R. Neubig
An Interhelical Salt Bridge Controls Flexibility and Inhibitor Potency For Regulators of G-protein Signaling (RGS) Proteins 4, 8, and 19
Mol. Pharmacol. 96:683-691 (2019) PDF
30. Yong Liu and Harish Vashisth
Conformational Dynamics and Interfacial Interactions of Peptide-appended Pillar[5]arene Water Channels in Biomimetic Membranes
Phys. Chem. Chem. Phys. 21:22711-22721 (2019) PDF
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29. Sanjib Paul, Nisanth N. Nair, and Harish Vashisth
Phase Space and Collective Variable Based Simulation Methods for Studies of Rare Events
Mol. Sim. 45:1273-1284 (2019) PDF
28. Kevin D. Schuster, Mohammadjavad Mohammadi, Karyn B. Cahill, Suzanne L. Matte, Alexis D. Maillet, Harish Vashisth, and Rick Cote
Pharmacological and molecular dynamics analyses of differences in inhibitor binding to human and nematode PDE4: implications for
management of parasitic nematodes
PLoS ONE 14: e0214554 (2019) PDF
27. Mohammadjavad Mohammadi, Hossein Mohammadiarani, Vincent Shaw, Richard R. Neubig, Harish Vashisth
Interplay of Cysteine Exposure and Global Protein Dynamics in Small-molecule Recognition by a Regulator of G-protein Signaling Protein
Proteins 87:146-156 (2019) PDF
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26. Yong Liu, Mohammadjavad Mohammadi, and Harish Vashisth
Diffusion network of CO in FeFe-Hydrogenase
J. Chem. Phys. 149:204108 (2018) PDF
25. Hossein Mohammadiarani, Vincent Shaw, Richard R. Neubig, Harish Vashisth
Interpreting Hydrogen-Deuterium Exchange Events in Proteins Using Atomistic Simulations: Case Studies on Regulators of G-protein
Signaling Proteins
J. Phys. Chem. B 122:9314-9323 (2018) PDF
24. Y. Shen, W. Song, DR Barden, T. Ren, C. Lang, H. Feroz, C. Henderson, P. Saboe, D. Tsai, H. Wang, PJ Butler, G. Bazan, W. Phillip, R. Hickey, P. Cremer,
Harish Vashisth, and Manish Kumar
Achieving high permeability and enhanced selectivity for Angstrom-scale separations using artificial water channel membranes
Nat. Commun. 9:2294 (2018) PDF
23. Daniel Ryan Barden and Harish Vashisth
Parameterization and atomistic simulations of biomimetic membranes
Faraday Discuss. 209:161-178 (2018) PDF
22. Structure and function of natural proteins for water transport: general discussion
Faraday Discuss. 209:83-95 (2018).
21. Biomimetic water channels: general discussion
Faraday Discuss. 209:205-229 (2018).
20. The modelling and enhancement of water hydrodynamics: general discussion
Faraday Discuss. 209:273-285 (2018).
19. Applications to water transport systems: general discussion
Faraday Discuss. 209:389-414 (2018).
18. Vincent Shaw, Hossein Mohammadiarani, Harish Vashisth, and Richard R. Neubig
Differential protein dynamics of regulators of G-protein signaling: Role in specificity of small-molecule inhibitors
J. Am. Chem. Soc. 140:3454-3460 (2018) PDF
2013-2017
17. Mohammadjavad Mohammadi and Harish Vashisth
Pathways and thermodynamics of oxygen diffusion in [FeFe]-Hydrogenase
J. Phys. Chem. B 121:10007-10017 (2017) PDF
16. Alex Dickson, Pratyush Tiwary, and Harish Vashisth
Kinetics of ligand binding through advanced computational approaches
Curr. Top. Med. Chem. 17:2626-2641 (2017) PDF
15. Hossein Mohammadiarani and Harish Vashisth
Insulin mimetic peptide S371 folds into a helical structure
J. Comput. Chem. 38:1158-1166 (2017) PDF
14. Hossein Mohammadiarani and Harish Vashisth
All-atom structural models of the transmembrane domains of insulin and type 1 insulin-like growth factor receptors
Front. Endocrinol. 7:68 (2016) PDF
13. Harish Vashisth
Theoretical and computational studies of peptides and receptors of the insulin family
Membranes 5:48-83 (2015) PDF
12. Harish Vashisth
Flexibility in the insulin receptor ectodomain enables docking of insulin in crystallographic conformation observed in hormone-bound
microreceptor
Membranes 4:730-746 (2014) PDF
11. Harish Vashisth, Georgios Skiniotis, and Charles L. Brooks III
Collective variable approaches for single molecule flexible fitting and enhanced sampling
Chem. Rev. 114:3353-3365 (2014) PDF
Highlighted in Chem. Rev. Editorial PDF
10. Harish Vashisth, Andrew J. Storaska, Richard R. Neubig, and Charles L. Brooks III
Conformational dynamics of a regulator of G-protein signaling protein reveals a mechanism of allosteric inhibition by a small molecule
ACS Chem. Biol. 8:2778-2784 (2013) PDF
Author highlights in ACS Chem. Biol. PDF
9. Harish Vashisth and Cameron F. Abrams
All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element
Proteins 81:1017-1030 (2013) PDF
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8. Harish Vashisth, Georgios Skiniotis, and Charles L. Brooks III
Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps
J. Phys. Chem. B 117:3738-3746 (2013) PDF
2008-2012
7. Harish Vashisth and Charles L. Brooks III
Conformational sampling of maltose-transporter components in Cartesian collective variables is governed by the low-frequency normal
modes
J. Phys. Chem. Lett. 3:3379-3384 (2012) PDF
6. Harish Vashisth, Georgios Skiniotis, and Charles L. Brooks III
Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps
Structure 20:1453-1462 (2012) PDF
5. Harish Vashisth, Luca Maragliano, and Cameron F. Abrams
DFG-flip in the insulin receptor kinase is facilitated by a helical intermediate state of the activation loop
Biophys. J. 102:1979-1987 (2012) PDF
4. B. S. Strunk, C. R. Loucks, M. Su, H. Vashisth, S. Cheng, J. Schilling, C. L. Brooks III, K. Karbstein, and G. Skiniotis
Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates
Science 333:1449-1453 (2011) PDF
3. Harish Vashisth and Cameron F. Abrams
All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor
J. Mol. Biol. 400:645-658 (2010) PDF
2. Harish Vashisth and Cameron F. Abrams
Docking of insulin to a structurally equilibrated insulin receptor ectodomain
Proteins 78:1531-1543 (2010) PDF
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1. Harish Vashisth and Cameron F. Abrams
Ligand escape pathways and (un)binding free energy calculations for the hexameric insulin-phenol complex
Biophys. J. 95:4194-4204 (2008) PDF