F. C. Kalutantirige, J. He, L. Yao, S. Cotty, S. Zhou, J. W. Smith, E. Tajkhorshid, C. M. Schroeder, J. S. Moore, H. An, X. Su, and Y. Li (2024) Beyond nothingness in the formation and functional relevance of voids in polymer films. Nat. Commun., 15:2852.

D. D. Dhavale, A. M. Barclay, C. G. Borcik, K. Basore, D. A. Berthold, I. R. Gordon, J. Liu, M. H. Milchberg, J. Y. O’Shea, M. J. Rau, Z. Smith, S. Sen, B. Summers, J. Smith, O. A. Warmuth, R. J. Perrin, J. S. Perlmutter, Q. Chen, J. A. J. Fitzpatrick, C. D. Schwieters, E. Tajkhorshid, C. M. RIenstra, and P. T. Kotzbauer (2024) Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue. Nat. Commun., 15:2750.

E. J. Shinn and E. Tajkhorshid (2024) Generating Concentration Gradients Across Membranes for Molecular Dynamics Simulations of Periodic Systems. Int. J. Mol. Sci., 25:3616.

B. Vallat, B. M. Webb, J. D. Westbrook, T. D. Goddard, C. A. Hanke, A. Graziadei, E. Peisach, A. Zalevsky, J. Sagendorf, H. Tangmunarunkit, S. Voinea, M. Sekharan, J. Yu, A. A. M. J. J. Bonvin, F. DiMaio, G. Hummer, J. Meiler, E. Tajkhorshid, T. E. Ferrin, C. L. Lawson, A. Leitner, J. Rappsilber, C. A. M. Seidel, C. M. Jeffries, S. K. Burley, J. C. Hoch, G. Kurisu, K. Morris, A. Patwardhan, S. Velankar, T. Schwede, J. Trewhella, C. Kesselman, H. M. Berman, and A. Sali (2024) IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J. Mol. Biol., 18:168546.

P. Roy, J. Maturano, H. Hasdemir, A. Lopez, F. Xu, J. Hellman, E. Tajkhorshid, D. Sarlah, and A. Das (2024) Elucidating the Mechanism of Metabolism of Cannabichromene by Human Cytochrome P450s. J. Nat. Prod.

J. Zhang, Y. Yu, X. Zou, Y. Du, Q. Liang, M. Gong, Y. He, J. Luo, D. Wu, X. Jiang, M. Sinclair, E. Tajkhorshid, H. Z. Chen, Z. Hou, Y. Zheng, L. F. Chen, and X. D. Yang (2024) WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination. Nucleic Acids Res., gkae161.

T. Gose, A. Rasouli, S. Dehghani-Ghahnaviyeh, P. C. Wen, Y. Wang, J. Lynch, Y. Fukuda, T. Shafi, R. C. Ford, E. Tajkhorshid, and J. D. Schultz (2024) Tumor-acquired somatic mutation affects conformation to abolish ABCG2-mediated drug resistance. Drug Resist. Updat., 73:101066.

H. Park, X. Yan, R. Zhu, E. A. Huerta, S. Chaudhuri, D. Cooper, I. Foster, and E. Tajkhorshid (2024) A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture. Commun. Chem., 7:21.

C. D. Radka, C. R. Grace, H. S. Hasdemir, Y. Li, C. C. Rodriguez, P. Rodrigues, M. L. Oldham, M. Z. Qayyum, A. Pitre, W. J. MacCain, R. C. Kalathur, E. Tajkhorshid, and O. Rock (2024) The carboxy terminus causes interfacial assembly of oleate hydratase on a membrane bilayer. J. Biol. Chem., 105627.

Q. Tang, M. Sinclair, H. S. Hasdemir, R. A. Stein, E. Karakas, E. Tajkhorshid, and H. S. Mchaourab (2023) Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. Nat. Commun., 14:7184.

Y. Zhang, O. Scubas, S. Pant, F. Heinrich, A. Vogel, J. Li, Y. Li, L. A. Clifton, S. Dam, K. Bacia, D. Huster, P. A. Randazzo, M. Losche, E. Tajkhorshid, and R. A. Byrd (2023) Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1. Nat. Commun., 14:7570.

W. Elwasif, W. Godoy, N. Hagerty, J. A. Harris, O. Hernandez, B. Joo, P. Kent, D. Lebrun-Grandie, E. Maccarthy, V. Melesse Vergara, B. Messer, R. Miller, S. Oral, S. Bastrakov, M. Bussman, A. Debus, K. Steiniger, J. Stephan, R. Widera, S. Bryngelson, H. Le Berre, A. Radhakrishnan, J. Young, S. Chandrasekaran, F. Ciorba, O. Simsek, K. Clark, F. Spiga, J. Hammond, J. Stone, D. Hardy, S. Keller, J. G. Piccinali, and C. Trott (2023) Application Experiences on a GPU-Accelerated Arm-based HPC Testbed. Association for Computing Machinery, HPC Asia '23 Workshops.

M. Spivak, J. E. Stone, J. Ribeiro, J. Saam, P. L. Freddolino, R. C. Bernardi, and E. Tajkhorshid (2023) VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. J. Chem. Inf. Model., 63:4664-4678.

S. Dey, A. Patel, N. Haloi, S. Srimayee, S. Paul, G. K. Barik, N. Akhtar, D. Shaw, G. Hazarika, B. M. Prusty, M. Kumar, M. K. Santra, E. Tajkhorshid, S. Bhattacharjee, and D. Manna (2023) Quinoline Thiourea-Based Zinc Ionophores with Antibacterial Activity. J. Med. Chem., 66:11078-11093.

D. Yang, Z, Zhao, E. Tajkhorshid, and E. Gouaux (2023) Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants. Proc. Natl. Acad. Sci. USA.

H. Park, R. Zhu, E. A. Huerta, S. Chaudhuri, E. Tajkhorshid, and D. Cooper (2023) End-to-end AI framework for interpretable prediction of molecular and crystal properties. Machine Learning: Science and Technology.

Y. Li, A. Acharya, L. Yang, J. Liu, E. Tajkhorshid, H. I. Zgurskaya, M. Jackson, and J. Gumbart (2023) Insights into substrate transport and water permeation in the mycobacterial transporter MmpL3. Biophys. J.

G. D. Galles, D. T. Infield, C. J. Clark, M. L. Hemshorn, S. Manikandan, F. Fazan, A. Rasouli, E. Tajkhorshid, J. D. Galpin, R. B. Cooley, R. A. Mehl, and C. A. Ahern (2023) Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells. Nat. Commun., 14:59.

A. Rasouli, Q. Yu, S. Dehghani-Ghahnaviyeh, and E. Tajkhorshid (2022) Differential dynamics and direct interaction of bound ligands with lipids in multidrug transporter ABCG2. Proc. Natl. Acad. Sci. USA, 120:e2213437120.

L. T. My Le, J. R. Thompson, S. Dehghani-Ghahnaviyeh, S. Pant, P. X. Dang, T. Kanikeyo, E. Tajkhorshid, and A. Alam (2022) Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms. EMBO Journal, 42:e111065.

L. Leisle, K. Lam, S. Dehghani-Ghahnaviyeh, E. Fortea, J. Galpin, C. A. Ahern, E. Tajkhorshid, and A. Accardi (2022) Backbone amides are key determinants of Cl- selectivity in CLC ion channels. Nat. Commun., 13:7508.

S. Dehghani-Ghahnaviyeh, Z. Zhao, and E. Tajkhorshid (2022) Lipid-mediated prestin organization in outer hair cell membranes and its implications in sound amplification. Nat. Commun., 13:6877.

H. Jeong, S. Clark, A. Goehring, S. Dehghani-Ghahnaviyeh, A. Rasouli, E. Tajkhorshid, and E. Gouaux (2022) Structures of the TMC-1 complex illuminate mechanosensory transduction. Nature, 610:796-803.

I. Singaram, A. Sharma, S. Pant, M. Lihan, M. J. Park, P. Buwaneka, Y. Hu, N. Mahmud, Y. M. Kim, V. Gevorgyan, I. Khan, E. Tajkhorshid, and W. Cho (2022) Targeting lipid-protein interaction for drug development: Development of a novel resistance-proof Syk inhibitor for acute myeloid leukemia. Nat. Chem. Biol.

R. Dastvan, A. Rasouli, S. Dehghani-Ghahnaviyeh, S. Gies, and E. Tajkhorshid (2022) Proton-driven alternating access in a spinster transporter, an emerging family of broad-specificity effux pumps. Nat. Commun., 13:5161.

A. Trifan, D. Gorgun, M. Salim, Z. Li, A. Brace, M. Zvyagin, H. Ma, A. Clyde, D. Clark, D. J. Hardy, T. Burnley, L. Huang, J. McCalpin, M. Emani, H. Yoo, J. Yin, A. Tsaris, V. Subbiah, T. Raza, J. Liu, N. Trebesch, G. Wells, V. Mysore, T. Gibbs, J. Phillips, S. C. Chennubhotla, I. Foster, R. Stevens, A. Anandkumar, V. Vishwanath, J. E. Stone, E. Tajkhorshid, S. A. Harris, and A. Ramanathan (2022) Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. The International Journal of High Performance Computing Applications.

M. P. Muller, J. H. Morrissey, and E. Tajkhorshid (2022) Molecular View into Preferential Binding of the Factor VII Gla Domain to Phosphatidic Acid. Biochemistry, 61:1694-1703.

M. S. Barhaghi, B. Crawford, G. Schwing, D. J. Hardy, J. E. Stone, L. Schwiebert, J. Potoff, G. R. Warner, and E. Tajkhorshid (2022) py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD. J. Chem. Theory Comput.

D. D. Meling, K. M. De La Torre, A. S. Arango, A. Gonsioroski, A. R.K. Deviney, A. M. Neff, M. J. Laws, G. R. Warner, E. Tajkhorshid, and J. A. Flaws (2022) Phthalate monoesters act through peroxisome proliferator-activated receptors in the mouse ovary. Reproductive Toxicology, 110:113-123.

K. Kapoor, T. Chen, and E. Tajkhorshid (2022) Post-translational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors. Proc. Natl. Acad. Sci. USA, 119:e2119761119.

D. J. Hardy, J. Choi, W. Jiang, and E. Tajkhorshid (2022) Experiences porting NAMD to the Data Parallel C++ programming model. Association for Computing Machinery, IWOCL22.

J. E. Stone, K. Griffin, J. Amstutz, D. E. Demarle, W. Sherman, and J. Guenther (2022) ANARI: A 3D Rendering API Standard. Comput. Sci. Eng.

K. Kapoor, S. Thangapandian, and E. Tajkhorshid (2022) Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins. Chem. Sci., 13:4150-4169.

Q. Wu, A. Akhter, S. Pant, E. Cho, J. X. Zhu, A. R. Garner, T. Ohyama, E. Tajkhorshid, D. J. van Meyel, and R. M. Ryan (2022) Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel activity and glial regulation of CNS function. J. Clin. Invest., e154891.

R. P. Sparks, W. Lawless, A. S. Arango, E. Tajkhorshid, and R. A. Fratti (2022) Use of Microscale Thermophoresis to Measure Protein-Lipid Interactions. J. Vis. Exp., 180:e60607.

S. Pant, Q. Wu, R. Ryan,and E. Tajkhorshid (2022) Microscopic Characterization of the Chloride Permeation Pathway in the Human Excitatory Amino Acid Transporter 1. ACS Chem. Neurosci., 13:776-785.

J. M. Gullett, M. G. Cuypers, C. R. Grace, S. Pant, C. Subramanian, E. Tajkhorshid, C. O. Rock, and S. W. White (2022) Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes. J. Biol. Chem., 298:101676.

H. Chen, D. Ogden, S. Pant, W. Cai, E. Tajkhorshid, M. Moradi, B. Roux, and C. Chipot (2022) A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls. J. Chem. Theory Comput. 18:1406-1422.

A. K. Vasan, N. Haloi, R. J. Ulrich, M. E. Metcalf, P. C. Wen, W. W. Metcalf, P. J. Hergenrother, D. Shukla, and E. Tajkhorshid (2022) Role of internal loop dynamics in antibiotic permeability of outer membrane porins. Proc. Natl. Acad. Sci. USA, 119:e2117009119.

J. S. Kim, A. S. Arango, S. Shah, W. R. Arnold, E. Tajkhorshid, and A. Das (2022) Anthracycline derivatives inhibit cardiac CYP2J2. J. Inorg. Biochem., 229:111722.

C. K. Chan, A. Singharoy, and E. Tajkhorshid (2022) Anionic lipids confine cytochrome c2 to the surface of bioenergetic membranes without compromising its interaction with redox partners. Biochemistry, 61:385-397.

G. Licari, S. Dehghani-Ghahnaviyeh, and E. Tajkhorshid (2022) Membrane Mixer: A toolkit for efficient shuffling of lipids in heterogeneous biological membranes. J. Chem. Inf. Model., 62: 986-996.

J. Vermaas, C. Mayne, E. Shinn, and E. Tajkhorshid (2022) Assembly and analysis of cell-scale membrane envelopes. J. Chem. Inf. Model., 62: 602-617.