Structural Bioinformatics, Biomolecular Simulations, and Artificial Intelligence
Je suis Research Assistant Professor au sein de la School of Systems Biology de George Mason University. Notre laboratoire développe et utilise des méthodes informatiques avancées pour étudier les mécanismes moléculaires. Notre expertise inclut la dynamique moléculaire par échange de répliques (replica exchange molecular dynamics, REMD), la perturbation d'énergie libre (free energy perturbation, FEP), la conception de médicaments de novo et l'intelligence artificielle. Les axes principaux de nos recherches portent sur l'interaction des peptides Aβ de la maladie d'Alzheimer et des peptides antimicrobiens avec les bicouches lipidiques.
Futurs étudiantsLes programmes de Master (MS) et de Doctorat (PhD) en bio-informatique et biologie computationnelle de GMU acceptent actuellement de nouvelles candidatures. Pour des informations générales sur la School of Systems Biology, veuillez consulter le site de la SSB. Pour plus de détails concernant les admissions aux cycles supérieurs et le processus de candidature, veuillez vous référer à la page des admissions de la SSB.
Dernières actualités
- Aug 2026New publication: Bowers, S. R., Lockhart, C., & Klimov, D. K. (2026) Replica exchange molecular dynamics with hydrogen mass repartitioning improves sampling of peptide binding to a lipid bilayer. J. Chem. Theory Comput. (accepted), doi: 10.1021/acs.jctc.6c01064
- Apr 2026New publication: Yi, F., Guo, J., Vo, T. T., Hetrick, B., Haikerwal, A., Zhou, Z., Sealey, L., He, S., Han, Y., Chilin, L., Spear, M., Yu, D., Kim, Y., Kashanchi, F., Zhou, T., Xu, X., Lockhart, C., & Wu, Y. (2026) Discovery of actinator, actin-derived bioactive peptides that modulate cytoskeleton and actin-related cellular activities. Sci. Adv. 12(16): eaeb5548, doi: 10.1126/sciadv.aeb5548
- Fév 2026Présentation d'affiche : Xie, L., Lockhart, C., Klimov, D. K., & Jafri, M. S. "Accurate prediction of cancer drug resistant variants using molecular simulation, machine learning, and network modeling." Biophysical Society 70th Annual Meeting, San Francisco, CA, February 2026.
- Jan 2026New publication: Bowers, S. R., Jeffries, W., Lockhart, C., & Klimov, D. K. (2026) Accelerating replica exchange molecular dynamics: A comparison of hydrogen mass repartitioning and light water models. J. Chem. Theory Comput. (accepted), doi: 10.1021/acs.jctc.5c01929
- Oct 2025New publication: Luo, X., Khayat, E., Bowers, S. R., Delfing, B. M., Lockhart, C., & Klimov, D. K. (2025) Free energy perturbation simulations measure the change in binding affinity of the Aβ25–35 peptide to the zwitterionic bilayer caused by oxidation. J. Chem. Inf. Model. 65(21): 12014-12026, doi: 10.1021/acs.jcim.5c02148
- Sep 2025New publication: Jeffries, W., Delfing, B. M., Laracuente, X. E., Luo, X., Olson, A., Foreman, K. W., Lee, K. H., Petruncio, G., De Benedictis, V., Paige, M. Kehn-Hall, K., Lockhart, C., & Klimov, D. K. (2025) Ligands binding diffusively to protein target act as inhibitors of protein-protein interactions. PLoS Comput. Biol. 21(9): e1013495, doi: 10.1371/journal.pcbi.1013495
- Aug 2025New publication: Xie, L., Lockhart, C., Klimov, D. K., & Jafri, M. S. (2025) Combining molecular dynamics and machine learning to predict drug resistance causing variants of BRAF in colorectal cancer. Molecules 30(17): 3556, doi: 10.3390/molecules30173556
- Aug 2025New publication: Fitz, A. R., Klimov, D. K., & Lockhart, C. (2025) Binding of antimicrobial peptide indolicidin to DMPC bilayer using replica-exchange molecular dynamics. J. Chem. Inf. Model. 65(17): 9251-9260, doi: 10.1021/acs.jcim.5c01153
- May 2025New publication: Han, Y., Sealey, L., Fu, Y., Delfing, B. M., Lockhart, C., Chilin, L., Tiwari, S., Jafri, M. S., Klimov, D. K., & Wu, Y. (2025) The decameric repeat (DR) of PSGL-1 functions as a basic antiviral unit in restricting HIV-1 infectivity. bioRxiv(posted), doi: 10.1101/2025.05.14.654117
- Mai 2025Présentation orale : Han, Y., Sealey, L., Fu, Y., Chilin, L., Tiwari, S., Lockhart, C., Delfing, B. M., Jafri, M. S., Klimov, D. K., & Wu, Y. "The decameric repeat of PSGL-1 functions as a basic antiviral unit in restricting HIV-1 infectivity." Retroviruses 50th Annual Meeting, Cold Spring Harbor, NY, May 2025.
- Apr 2025New publication: Laracuente, X. E., Delfing, B. M., Luo, X., Olson, A., Jeffries, W., Bowers, S. R., Foreman, K. W., Lee, K.-H., Paige, M., Kehn-Hall, K., Lockhart, C., & Klimov, D. K. (2025) Applying absolute free energy perturbation molecular dynamics to diffusively binding ligands. J. Chem. Theory Comput. 21(8): 4286-4298, doi: 10.1021/acs.jctc.5c00121
- Avr 2025Présentation orale : Tiwari, S., Delfing, B. M., Han, Y., Lockhart, C., Haikerwal, A., Jafri, M. S., Klimov, D. K., & Wu, Y. "PSGL-1 excludes HIV Env from virion surface through spatial hindrance involving structural folding of the decameric repeats." HIV Dynamics and Replication Program 28th Think Tank Meeting, Frederick, MD, April 2025.
- Mar 2025New publication: He, S., Haikerwal, A., Tiwari, S., Dabbagh, D., Alam, M. Z., Yoon, J. L., Hetrick, B., Han, Y., Shan, L., Lockhart, C., & Wu, Y. (2025) CD34 serves as an intrinsic innate immune guardrail protecting stem cells from replicating retroviruses. bioRxiv(posted), doi: 10.1101/2025.03.15.643450
- Fév 2025Présentation d'affiche : Lockhart, C., Delfing, B. M., Laracuente, X. E., Olson, A., Luo, X., Jeffries, W., Foreman, K. W., Petruncio, G., Lee, K.-H., Paige, M., Kehn-Hall, K., & Klimov, D. K. "Understanding the molecular mechanism of Venezuelan equine encephalitis virus inhibition." Biophysical Society 69th Annual Meeting, Los Angeles, CA, February 2025.
- Jan 2025New publication: Xie, L., Lockhart, C., Bowers, S. R., Klimov, D. K., & Jafri, M. S. (2025) Structural analysis of amylin and amyloid β peptide signaling in Alzheimer’s disease. Biomolecules 15(1): 89, doi: 10.3390/biom15010089
- Dec 2024New publication: Tiwari, S., Delfing, B. M., Han, Y., Lockhart, C., Haikerwal, A., Waheed, A. A., Freed, E. O., Jafri, M. S., Klimov, D. K., & Wu, Y. (2024) PSGL-1 excludes HIV Env from virion surface through spatial hindrance involving structural folding of the decameric repeats. bioRxiv(posted), doi: 10.1101/2024.12.28.630612v1
- Dec 2024New publication: Goldberg, J. F., de Filippi, C. R., Lockhart, C., McNair, E. R., Sinha, S., Kong, H., Najjar, S. S., Lohmar, B. J., Tchoukina, I., Shah, K., Feller, E., Hsu, S., Rodrigo, M. E., Jang, M., Marboe, C. C., Berry, G. J., Valantine, H. A., Agbor-Enoh, A., & Shah, P. (2024) Proteomics in acute heart transplant rejection, on behalf of the GRAfT Investigators. Transplantation(in press), doi: 10.1097/TP.0000000000005258
- Sep 2024New publication: Delfing, B. M., Laracuente, X. E., Luo, X., Olson, A., Jeffries, W., Foreman, K. W., Paige, M., Kehn-Hall, K., Lockhart, C., & Klimov, D. K. (2024) Binding of inhibitors to nuclear localization signal peptide from Venezuelan equine encephalitis virus capsid protein explored with all-atom replica exchange molecular dynamics. ACS Omega 9(38): 40259-40268, doi: 10.1021/acsomega.4c06981
- Août 2024Présentation d'affiche : Ganji, V. & Lockhart, C. "Screening aggregation breakers of Alzheimer's disease Aβ protofibrils using AutoDock CrankPep." ASSIP Research Celebration, Manassas, VA, August 2024.
- Jun 2024New publication: Delfing, B. M., Laracuente, X. E., Jeffries, W., Luo, X., Olson, A., Foreman, K. W., Petruncio, G., Lee, K. H., Paige, M., Kehn-Hall, K., Lockhart, C., & Klimov, D. K. (2024) Competitive binding of viral nuclear localization signal peptide and inhibitor ligands to importin-α nuclear transport protein. J. Chem. Inf. Model. 64(13): 5262-5272, doi: 10.1021/acs.jcim.4c00626
- Mai 2024Nouvelle du laboratoire : Accueil de V. Ganji au laboratoire en tant que stagiaire ASSIP (été 2024).
- Feb 2024New publication: Bowers, S. R., Lockhart, C., & Klimov, D. K. (2024) Binding and dimerization of PGLa peptides in anionic lipid bilayer studied by replica exchange molecular dynamics. Sci. Rep. 14: 4972, doi: 10.1038/s41598-024-55270-8
- Sep 2023New publication: Bowers, S. R., Lockhart, C., & Klimov, D. K. (2023) Replica exchange with hybrid tempering efficiently samples PGLa peptide binding to anionic bilayer. J. Chem. Theory Comput. 19(18): 6532-6550, doi: 10.1021/acs.jctc.3c00787
- Sep 2023New publication: Delfing, B. M., Laracuente, X. E., Olson, A., Foreman, K. W., Paige, M., Kehn-hall, K., Lockhart, C., & Klimov, D. K. (2023) Binding of viral nuclear localization signal peptides to importin-α nuclear transport protein. Biophys. J. 122(17): 3476-3488, doi: 10.1016/j.bpj.2023.07.024
- Aug 2023New publication: Lockhart, C., Luo, X., Olson, A., Delfing, B. M., Laracuente, X. E., Foreman, K. W., Paige, M., Kehn-Hall, K., & Klimov, D. K. (2023) Can free energy perturbation simulations coupled with replica-exchange molecular dynamics study ligands with distributed binding sites? J. Chem. Inf. Model. 63(15): 4791-4802, doi: 10.1021/acs.jcim.3c00631
- Août 2023Présentation d'affiche : Díaz Delgado, M. J. & Lockhart, C. "Network analysis of replica exchange simulations." ASSIP Research Celebration, Manassas, VA, August 2023.
- Mai 2023Nouvelle du laboratoire : Accueil de M. J. Díaz Delgado, S. Jain, M. Chawla et K. Gohil au laboratoire en tant que stagiaires ASSIP (été 2023).
- Mar 2023New publication: Delfing, B. M., Olson, A., Laracuente, X. E., Foreman, K. W., Paige, M., Kehn-Hall, K., Lockhart, C., & Klimov, D. K. (2023) Binding of Venezuelan equine encephalitis virus inhibitors to importin-α receptors explored with all-atom replica exchange molecular dynamics. J. Phys. Chem. B 127(14): 3175-3186, doi: 10.1021/acs.jpcb.3c00429
- Jan 2023New publication: Khayat, E., Delfing, B. M., Laracuente, X. E., Olson, A., Lockhart, C., & Klimov, D. K. (2023) Lysine acetylation changes the mechanism of Aβ25-35 peptide binding and dimerization in the DMPC bilayer. ACS Chem. Neurosci. 14(3): 494-505, doi: 10.1021/acschemneuro.2c00722
- Dec 2022New publication: Vergilio, J., Lockhart, C., & Klimov, D. K. (2022) De novo transmembrane aggregation of Aβ10-40 peptides in anionic lipid bilayer. J. Chem. Inf. Model. 62(23): 6228-6241, doi: 10.1021/acs.jcim.2c01192
- Mai 2022Nouvelle du laboratoire : Accueil de K. Gohil au laboratoire en tant que stagiaire ASSIP (été 2022).
- Mar 2022New publication: Bowers, S. R., Klimov, D. K., & Lockhart, C. (2022) Mechanisms of binding of antimicrobial peptide PGLa to DMPC/DMPG membrane. J. Chem. Inf. Model. 62(6): 1525-1537, doi: 10.1021/acs.jcim.1c01518
- Aug 2021New publication: Khayat, E., Lockhart, C., Delfing, B. M., Smith, A. K., & Klimov, D. K. (2021) Met35 oxidation hinders Aβ25-35 peptide aggregation within the dimyristoylphosphatidylcholine bilayer. ACS Chem. Neurosci. 12(17): 3225-3236, doi: 10.1021/acschemneuro.1c00407
- Mar 2021New publication: Siwy, C. M., Delfing, B. M., Lockhart, C., Smith, A. K., & Klimov, D. K. (2021) Partitioning of Aβ peptide fragments into blood–brain barrier mimetic bilayer. J. Phys. Chem. B 125(10): 2658-2676, doi: 10.1021/acs.jpcb.0c11253
- Mar 2020New publication: Lockhart, C., Smith, A. K., & Klimov, D. K. (2020) Three popular force fields predict consensus mechanism of Aβ peptide binding to the DMPC bilayer. J. Chem. Inf. Model. 60(4): 2282-2293, doi: 10.1021/acs.jcim.0c00096
- Fév 2020Présentation d'affiche : Lockhart, C., Smith, A. K., & Klimov, D. K. "Methionine oxidation alters the mechanism of Aβ interaction with DMPC bilayers." Biophysical Society 64th Annual Meeting, San Diego, CA, February 2020.
- Nov 2019New publication: Smith, A. K., Khayat, E., Lockhart, C., & Klimov, D. K. (2019) Do cholesterol and sphingomyelin change the mechanism of Aβ25-35 peptide binding to zwitterionic bilayer? J. Chem. Inf. Model. 59(12): 5207-5217, doi: 10.1021/acs.jcim.9b00763
- Apr 2019New publication: Lockhart, C., Smith, A. K., & Klimov, D. K. (2019) Methionine oxidation changes the mechanism of Aβ peptide binding to the DMPC bilayer. Sci. Rep. 9(5947): 1-12, doi: 10.1038/s41598-019-42304-9
- Sep 2017New publication: Lockhart, C. & Klimov, D. K. (2017) Cholesterol changes the mechanism of Aβ peptide binding to the DMPC bilayer. J. Chem. Inf. Model. 57(10): 2554-2565, doi: 10.1021/acs.jcim.7b00431
- Fév 2017Présentation d'affiche : Lockhart, C. & Klimov, D. K. "Probing the binding of Aβ peptides to lipid bilayers." Biophysical Society 61st Annual Meeting, New Orleans, LA, February 2017.
- Jan 2017New publication: Siwy, C. M., Lockhart, C., & Klimov, D. K. (2017) Is the conformational ensemble of Alzheimer's Aβ10-40 peptide force field dependent? PLoS Comput. Biol. 13(1): e1005314, doi: 10.1371/journal.pcbi.1005314
- Aug 2016New publication: Smith, A. K., Lockhart, C., & Klimov, D. K. (2016) Does replica exchange with solute tempering efficiently sample Aβ peptide conformational ensembles? J. Chem. Theory Comput. 12(10): 5201-5214, doi: 10.1021/acs.jctc.6b00660
- Mar 2016New publication: Lockhart, C. & Klimov, D. K. (2016) The Alzheimer's disease Aβ peptide binds to the anionic DMPS lipid bilayer. Biochim. Biophys. Acta 1858(6): 1118-1128, doi: 10.1016/j.bbamem.2016.03.001
- Aug 2015New publication: Lockhart, C. (2015) Molecular dynamics simulations of peptides relevant to Alzheimer's disease PhD Dissertation, George Mason University
- Aug 2015New publication: Lockhart, C., O'Connor, J., Armentrout, S., & Klimov, D. K. (2015) Greedy replica exchange algorithm for heterogeneous computing grids. J. Mol. Model. 21(9): 243, doi: 10.1007/s00894-015-2763-5
- Apr 2015New publication: Lockhart, C. & Klimov, D. K. (2015) Calcium enhances binding of Aβ monomer to DMPC bilayer. Biophys. J. 108(7): 1807-1818, doi: 10.1016/j.bpj.2015.03.001
- Fév 2015Présentation d'affiche : Lockhart, C. & Klimov, D. K. "Binding of Aβ monomer to DMPC bilayer using isobaric-isothermal replica-exchange molecular dynamics." Biophysical Society 59th Annual Meeting, Baltimore, MD, February 2015.
- Jul 2014New publication: Lockhart, C. & Klimov, D. K. (2014) Binding of Aβ peptide creates lipid density depression in DMPC bilayer. Biochim. Biophys. Acta 1838(10): 2678-2688, doi: 10.1016/j.bbamem.2014.07.010
- Feb 2014New publication: Lockhart, C. & Klimov, D. K. (2014) Alzheimer's Aβ10-40 peptide binds and penetrates DMPC bilayer: an isobaric-isothermal replica exchange molecular dynamics study. J. Phys. Chem. B 118(10): 2638-2648, doi: 10.1021/jp412153s
- Sep 2013New publication: Lockhart, C. & Klimov, D. K. (2013) Revealing hidden helix propensity in Aβ peptide by molecular dynamics simulations. J. Phys. Chem. B 117(40): 12030-12038, doi: 10.1021/jp407705j
- Dec 2012New publication: Lockhart, C. & Klimov, D. K. (2012) Molecular interactions of Alzheimer's biomarker FDDNP with Aβ peptide. Biophys. J. 103(11): 2341-2351, doi: 10.1016/j.bpj.2012.10.003
- Oct 2012New publication: Lockhart, C., Kim, S., & Klimov, D. K. (2012) Explicit solvent molecular dynamics simulations of Aβ peptide interacting with ibuprofen ligands. J. Phys. Chem. B 116(43): 12922-12932, doi: 10.1021/jp306208n
- Jul 2011New publication: Lockhart, C., Kim, S., Kumar, R., & Klimov, D. K. (2011) Does amino acid sequence determine the properties of Aβ dimer? J. Chem. Phys. 135: 35103, doi: 10.1063/1.3610427