​Peer-Reviewed Journal Articles

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1. M.D. Polêto and J.A. Lemkul (2024) “Structural and Electronic Properties of Polyethylene Terepththalate (PET) from Polarizable Molecular Dynamics Simulations” Macromolecules. In Press. [DOI]
    

2. J.A. Lemkul (2024) “Introductory Tutorials for Simulating Protein Dynamics with GROMACS” J. Phys. Chem. B. 128 (39): 9418-9435. (PMC11457149) [DOI]
    

3. W. Hwang, S.L. Austin, A. Blondel, E.D. Boittier, S. Boresch, M. Buck, J. Buckner, A. Caflisch, H.-T. Chang, X. Cheng, Y.K. Choi, J.-W. Chu, M. Crowley, Q. Cui, A. Damjanovic, Y. Deng, M. Devereux, X. Ding, M. Feig, J. Gao, D.R. Glowacki, J.E. Gonzales II, M.B. Hamaneh, E. Harder, R.L. Hayes, J. Huang, Y. Huang, P. Hudson, W. Im, S.M. Islam, W. Jiang, M.R. Jones, S. Käser, F.L. Kearns, N.R. Kern, J.B. Klauda, T. Lazaridis, J. Lee, J.A. Lemkul, X. Liu, Y. Luo, A.D. MacKerell Jr., D.T. Major, M. Meuwly, K. Nam, L. Nilsson, V. Ovchinnikov, E. Paci, S. Park, R.W. Pastor, C.B. Post, S. Prasad, J. Pu, Y. Qi, T. Rathinavelan, D.R. Roe, B. Roux, C.N. Rowley, J. Shen, A.C. Simmonett, A.J. Sodt, K. Töpher, M. Upadhyay, A. van der Vaart, L.I. Vazquez-Salazar, R.M. Venable, H.L. Woodcock, Y. Wu, C.L. Brooks III, B.R. Brooks, and M. Karplus. “CHARMM at 45: Enhancements in accessibility, functionality, and speed” J. Phys. Chem. B. In Press. (Virtual Special Issue: “Recent Advances in Simulation Software and Force Fields”) [DOI]
    

4. J.M. Montgomery and J.A. Lemkul (2024) “Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer” J. Phys. Chem. B 128 (30): 7385-7400. (PMC11301690) [DOI]
    

5. M.D. Polêto, K.D. Allen, and J.A. Lemkul (2024) “Structural dynamics of the methyl-coenzyme M reductase active site are influenced by coenzyme F430 modifications” Biochemistry, 63 (14): 1783-1794. (PMC11256747) [DOI]
    

6. H.M. Michel and J.A. Lemkul (2024) “Base Pair Dynamics, Electrostatics, and Thermodynamics at the LTR-III Quadruplex:Duplex Junction” Biophys. J. 123 (9): 1129-1138. (PMC11079942) [DOI]
    

7. D.S. Davidson and J.A. Lemkul (2024) “Pyroglutamylation Modulates Electronic Properties and the Conformational Ensemble of the Amyloid β-Peptide.” Proteins: Struct., Funct. & Bioinf. 92 (7): 842-853. (PMC11147713) [DOI]
    

8. M.D. Polêto and J.A. Lemkul (2023) “Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes.” J. Chem. Inf. Model. 63 (21): 6851-6862. (PMC10841373) [DOI]
    

9. A.F. Wacha and J.A. Lemkul (2023) “charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS.” J. Chem. Inf. Model. 63 (14): 4246-4252. (PMC109369483) [DOI]
    

10. N. Giacon, E. Lo Cascio, D.S. Davidson, M.D. Polêto, J.A. Lemkul, V. Pennacchietti, L. Pagano, C. Zamparelli, A. Toto, and A. Arcovito (2023) “Structural and functional insights on the interaction between SARS-CoV-2 E protein and ZO1-PDZ2.” Comput. Struct. Biotechnol. J. 21: 3259-3271. (PMC10210826) [DOI]
     

11. B. Grupp, J.A. Lemkul, and T. Gronemeyer (2023) “An in silico approach to determine inter-subunit affinities in human septin complexes.” Cytoskeleton 80 (7-8): 141-152. [DOI]
     

12. D.S. Davidson, J.A. Kraus, J.M. Montgomery, and J.A. Lemkul (2022) “Effects of Familial Alzheimer’s Disease Mutations on the Folding Free Energy and Dipole-Dipole Interactions of the Amyloid β-Peptide” J. Phys. Chem. B 126 (39): 7552-7566. (PMC9547858) [DOI]
     

13. A.M. Salsbury, H.M. Michel, and J.A. Lemkul (2022) "Ion-Dependent Conformational Plasticity of Telomeric G-Hairpins and G-Quadruplexes" ACS Omega 7 (27): 23368-23379. (PMC9280957) [DOI]
     

14. A.N. Corrigan and J.A. Lemkul (2022) “Electronic Polarization at the Interface Between the p53 Transactivation Domain and Two Binding Partners” J. Phys. Chem. B 126 (26): 4814-4827. (PMC9267131) [DOI]
     

15. K.M. King, A.K. Sharp, D.S. Davidson, A.M. Brown, and J.A. Lemkul (2022) “Impact of Electronic Polarization on Preformed, β-Sheet Rich Homogenous and Heterogenous Amyloid Oligomers” J. Comput. Biophys. Chem. 21 (4): 449-460. (PMC9216210) [DOI]
     

16. M.D. Polêto and J.A. Lemkul (2022) "TUPÃ: Electric field analyses for molecular simulations" J. Comput. Chem. 43 (16): 1113-1119.  (PMC9098685) [DOI]
     

17. M.D. Polêto and J.A. Lemkul (2022) "Integration of experimental data and use of automated fitting methods in developing protein force fields" Comms. Chem. 5: 38. (PMC8979544) [DOI]
     

18. A.A. Kognole, J. Lee, S.-J. Park, S. Jo, P. Chatterjee, J.A. Lemkul, J. Huang, A.D. MacKerell Jr., and W. Im (2022) “CHARMM-GUI Drude Prepper for Molecular Dynamics Simulation Using the Classical Drude Polarizable Force Field” J. Comput. Chem. 43 (5): 359-375. (PMC8741736) [DOI]
     

19. A.M. Salsbury and J.A. Lemkul (2021) "Cation Competition and Recruitment around the c-kit1 G-Quadruplex Using Polarizable Simulations." Biophys. J. 120 (11): 2249-2261. (PMC8390831) [DOI]
     

20. A.M. Salsbury and J.A. Lemkul (2021) "Recent Developments in Empirical Atomistic Force Fields for Nucleic Acids and Applications to Studies of Folding and Dynamics." Curr. Opin. Struct. Biol. 67: 9-17. (PMC7965779) [DOI]
     

21. B.D. Ratnasinghe, A.M. Salsbury, and J.A. Lemkul (2020) “Ion Binding Properties and Dynamics of the bcl-2 G-Quadruplex Using a Polarizable Force Field.” J. Chem. Inf. Model. 60 (12): 6476-6488. (PMC7775346) [DOI]
     

22. A.M. Salsbury, T.J. Dean, and J.A. Lemkul (2020) “Polarizable Molecular Dynamics Simulations of Two c-kit Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling.” J.Chem. Theory Comput. 16 (5): 3430-3444. (PMC7221321) [DOI]
     

23. J.A. Lemkul (2020) “Same Fold, Different Properties: Polarizable Molecular Dynamics Simulations of Telomeric and TERRA G-Quadruplexes” Nucleic Acids Res. 48 (2): 561-575. (PMC6954416) [DOI] 
     

24. R. Pawlak, J.G. Vilhena, P. D’Astolfo, X. Liu, G. Prampolini, T. Meier, T. Glatzel, J.A. Lemkul, R. Häner, S. Decurtins, A. Baratoff, R. Pérez, S.-X. Liu, and E. Meyer (2020) “Sequential Bending and Twisting of C-C Bonds by Mechanical Lifting of a Pre-Adsorbed Polymer” Nano Lett. 20 (1): 652-657. [DOI]
     

25. A.M. Salsbury, A.M. Brown, and J.A. Lemkul (2019) “Integrating Scientific Programming in Communities of Practice for Students in the Life Sciences.” Proceedings of Practice & Experience in Advanced Research Computing (PEARC19), 6 pp. (Honorable Mention in “Workforce Development and Diversity” paper category)
     

26. A. Umana, J.A. Lemkul, and D.J. Slade (2019) "Complete genome of Fusobacterium necrophurm subsp. necrophorum ATCC 25286." Microbiol. Resour. Announc. 8 (8): e00025-19. [DOI]
     

27. A.M. Salsbury and J.A. Lemkul (2019) "Molecular Dynamics Simulations of the c-kit1 Promoter G-Quadruplex: Importance of Electronic Polarization on Stability and Ion Cooperativity." J. Phys. Chem. B 123 (1): 148-159. [DOI]
     

28. J.A. Lemkul (2019) "From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0]." Living J. Comp. Mol. Sci. 1 (1): 5068. [DOI]
     

29. D. van der Spoel, M.M. Ghahremanpour, and J.A. Lemkul (2018) "Small Molecule Thermochemistry: A Tool for Empirical Force Field Development." J. Phys. Chem. A 122 (45): 8982-8988. [DOI]
     

30. J.A. Lemkul and A.D. MacKerell, Jr. (2018) "Polarizable Force Field for RNA Based on the Classical Drude Oscillator." J. Comput. Chem. 39 (32): 2624-2646. (PMC6284239) [DOI]
     

31. D.S. Davidson, A.M. Brown, and J.A. Lemkul (2018) "Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations." J. Mol. Biol. 430 (20): 3819-3834. [DOI] (F1000 Prime recommended article)
     

32. B.E. Sanders, A. Umana, J.A. Lemkul, and D.J. Slade (2018) “FusoPortal: An interactive repository of hybrid MinION-sequenced Fusobacterium genomes improves gene identification and characterization.” mSphere. 3: e00228-18. [DOI]
     

33. J. Huang, J.A. Lemkul, P.K. Eastman, and A.D. MacKerell, Jr. (2018) "Molecular Dynamics Simulations Using the Drude Polarizable Force Field on GPUs with OpenMM: Implementation, Validation, and Benchmarks." J. Comput. Chem. 39 (21) 1682-1689. [DOI]
     

34. L. R. Hollingsworth, J.A. Lemkul, D.R. Bevan, and A.M. Brown (2018) "HIV-1 Env Transmembrane Domain Dynamics Are Modulated by Lipid, Water, and Ion Interactions." Biophys. J. 115 (1): 84-94. [DOI]
     

35. E.H. Klontz, A.D. Tomich, S. Günther, J.A. Lemkul, D. Deredge, Z. Silverstein, J.F. Shaw, C. McElheny, Y. Doi, P. Wintrode, A.D. MacKerell, Jr., N. Sluis-Cremer, and E.J. Sundberg (2017) “Structure and dynamics of FosA-mediated fosfomycin resistance in Klebsiella pneumonia and Escherichia coli.” Antimicrob. Agents and Chemother. 61 (11): e01572-17. (PMC5655077) [DOI]
     

36. J.A. Lemkul and A.D. MacKerell, Jr. (2017) “Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.” J. Chem. Theory Comput. 13 (5): 2053-2071. (PMC5484419) [DOI]
     

37. J.A. Lemkul and A.D. MacKerell, Jr. (2017) “Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.” J. Chem. Theory Comput. 13 (5): 2072-2085. (PMC5485260) [DOI]
     

38. J.A. Lemkul and A.D. MacKerell, Jr. (2016) “Balancing Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model.” J. Phys. Chem. B 120 (44): 11436-11448. (PMC5148688) [DOI]
     

39. J.A. Lemkul, S.K. Lakkaraju, and A.D. MacKerell, Jr. (2016) “Characterization of Mg2+ Distributions around RNA in Solution.” ACS Omega 1 (4): 680-688. (PMC5088455) [DOI]
     

40. I. Soteras, F.-Y. Lin, K. Vanommeslaeghe, J.A. Lemkul, K. A. Armacost, C.L. Brooks III, and A.D. MacKerell, Jr. (2016) “Parametrization of Halogen Bonds in the CHARMM General Force Field: Improved Treatment of Ligand-Protein Interactions.” Bioorg. Med. Chem. 24 (20): 4812-4825. (PMC5053860) [DOI]
     

41. J.A. Lemkul, J. Huang, B. Roux, and A.D. MacKerell, Jr. (2016) “An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.” Chem. Rev. 116 (9): 4983-5013. (PMC4865892) [DOI]
     

42. J. Lee, X. Cheng, J. Swails, M.S. Yeom, P. Eastman, J.A. Lemkul, S. Wei, J. Buckner, J.C. Jeong, Y. Qi, S. Jo, V. Pande, D.A. Case, C.L. Brooks III, A.D. MacKerell, Jr., J.B. Klauda, and W. Im (2016) “CHARMM-GUI Input Generation for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM Force Fields.” J. Chem. Theory Comput. 12 (1): 405-413. (PMC4712441) [DOI]
     

43. S.K. Lakkaraju, J.A. Lemkul, J. Huang, and A.D. MacKerell, Jr. (2016) “DIRECT-ID: An Automated Method to Identify and Quantify Conformational Variations - Application to β2-adrenergic GPCR.” J. Comput. Chem. 37 (4): 416-425. (PMC4756637) [DOI]
     

44. J.A. Lemkul, J. Huang, and A.D. MacKerell, Jr. (2015) “Induced Dipole-Dipole Interactions Influence Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides.” J. Phys Chem. B 119 (51): 15574-15582. (PMC4690896) [DOI]
     

45. J.A. Lemkul, B. Roux, D. van der Spoel, and A.D. MacKerell, Jr. (2015) “Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model.” J. Comput. Chem. 36 (19): 1473-1479. (PMC4481176) [DOI]
     

46. J.A. Lemkul, S.N. Lewis, J. Bassaganya-Riera, and D.R. Bevan (2015) “Phosphorylation of PPARγ Affects Collective Motions of the PPARγ-RXRα-DNA Complex.” PLOS ONE. 10 (5): e0123984. [DOI]
     

47. S.R. Gerben, J.A. Lemkul, A.M. Brown, and D.R. Bevan (2014) “Comparing Atomistic Molecular Mechanics Force Fields for a Difficult Target: A Case Study of the Amyloid β-Peptide.” J. Biomol. Struct. Dyn. 32 (11): 1817-1832. [DOI]
     

48. J.A. Lemkul, A. Savelyev, and A.D. MacKerell, Jr. (2014) “Induced Polarization Influences the Fundamental Forces in DNA Base Flipping.” J. Phys. Chem. Lett. 5 (12): 2077-2083. (PMC4064933) [DOI] [ACS LiveSlides]
     

49. D.G.S. Capelluto, X. Zhao, A. Lucas, J.A. Lemkul, S. Xiao, X. Fu, F. Sun, D.R. Bevan, and C.V. Finkielstein (2014) “Biophysical and molecular dynamics studies of phosphatidic acid binding to the Dvl-2 DEP domain.” Biophys. J. 106 (5): 1101-1111. [DOI]
     

50. A.M. Brown, J.A. Lemkul, N. Schaum, and D.R. Bevan (2014) “Simulations of Monomeric Amyloid β-Peptide (1-40) with Varying Solution Conditions and Oxidation State of Met35: Implications for Aggregation.” Arch. Biochem. Biophys. 545 (1): 44-62. [DOI]
     

51. J.A. Lemkul and D.R. Bevan (2013) “Aggregation of Alzheimer’s Amyloid β-Peptide in Biological Membranes: A Molecular Dynamics Study.” Biochemistry. 52 (29): 4971-4980. [DOI]
     

52. J.A. Lemkul and D.R. Bevan (2012) “The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease.” ACS Chem. Neurosci. 3 (11): 845-856. [DOI] [Cover Art]
     

53. J.A. Lemkul and D.R. Bevan (2012) “Morin Inhibits the Early Stages of Amyloid β-Peptide Aggregation by Altering Tertiary and Quaternary Interactions to Produce ‘Off-Pathway’ Structures.” Biochemistry. 51 (30): 5990-6009. [DOI]
     

54. J.A. Lemkul and D.R. Bevan (2011) “Lipid Composition Influences the Release of Alzheimer’s Amyloid β-Peptide from Membranes.” Protein Sci. 20 (9): 1530-1545. [DOI]
     

55. J.A. Lemkul and D.R. Bevan (2011) “Characterization of Interactions Between PilA from Pseudomonas aeruginosa Strain K and a Model Membrane.” J. Phys. Chem. B 115 (24): 8004-8008. [DOI]
     

56. J.A. Lemkul, W.J. Allen, and D.R. Bevan (2010) “Practical Considerations for Building GROMOS-Compatible Small Molecule Topologies.” J. Chem. Inf. Model. 50 (12): 2221-2235. [DOI]
     

57. P. Mehere, Q. Han, J.A. Lemkul, C.J. Vavricka, H. Robinson, D.R. Bevan, and J. Li (2010) “Tyrosine Aminotransferase: biochemical and structural properties and molecular dynamics simulations.” Protein & Cell 1 (11): 1023-1032. [DOI]
     

58. J.A. Lemkul and D.R. Bevan (2010) “Destabilizing Alzheimer’s Aβ42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations.” Biochemistry. 49 (18): 3935-3946. [DOI]
     

59. J.A. Lemkul and D.R. Bevan (2010) “Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics” J. Phys. Chem. B 114 (4): 1652-1660. [DOI]
     

60. W.J. Allen, J.A. Lemkul, and D.R. Bevan (2009) “GridMAT-MD: A Grid-based Membrane Analysis Tool for Use With Molecular Dynamics.”  J. Comput. Chem. 30 (12): 1952-1958. [DOI]
     

61. J.A. Lemkul and D.R. Bevan (2009) “Perturbation of membranes by the amyloid β-peptide – a molecular dynamics study.” FEBS J. 276 (11): 3060-3075. [DOI]
     

62. J.A. Lemkul and D.R. Bevan (2008) “A Comparative Molecular Dynamics Analysis of the Amyloid β-Peptide in a Lipid Bilayer.” Arch. Biochem. Biophys. 470 (1): 54-63. [DOI]

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​Book Chapters

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1. J.A. Lemkul (2021) "Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model" In Methods in Molecular Biology. J. Mourão, I. Moreira, and M. Machuquiero, Eds. 2315: 219-240. [DOI]
    

2. J.A. Lemkul (2020) "Pairwise-additive and polarizable atomistic force fields for molecular dynamics simulations of proteins" Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly. In Progress in Molecular Biology and Translational Science. B. Strodel and B. Barz, Eds. 170: 1-71. [DOI]

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