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  1. Addala, S., Vissapragada, M., Aggunna, M., Mukala, N., Lanka, M., Gampa, S., Sodasani, M., Chintalapati, J., Kamidi, A., Veeranna, R. P., Yedidi, R. S.* Success of Current COVID-19 Vaccine Strategies vs. the Epitope Topology of SARS-CoV-2 Spike Protein-Receptor Binding Domain (RBD): A Computational Study of RBD Topology to Guide Future Vaccine Design. Vaccines. 2022; 10(6):841. (*Corresponding author)

  2. Amano, M., Yedidi, R. S., Salcedo-Gomez, P. M., Hayashi, H., Hasegawa, K., Martyr, C. D., Ghosh, A. K., Mitsuya, H. Fluorine Modifications Contribute to Potent Antiviral Activity against Highly Drug-Resistant HIV-1 and Favorable Blood-Brain Barrier Penetration Property of Novel Central Nervous System-Targeting HIV-1 Protease Inhibitors In Vitro. Antimicrob Agents Chemother., 66(2):e0171521, 2022. (Related PDB IDs: 6UWB and 6UWC).

  3. Amano, M., Salcedo-Gomez, P. M., Yedidi, R. S., Zhao, R., Hayashi, H., Hasegawa, K., Nakamura, T., Martyr, C. D., Ghosh, A. K., Mitsuya, H. Novel central nervous system (CNS)-targeting protease inhibitors for drug-resistant HIV infection and HIV-associated CNS complications. Antimicrob Agents Chemother., 63:(7), pii:e00466-19, 2019. (Related PDB IDs: 6D0E and 6D0D).

  4. Sasidharan, P., Balo, A. R., Enenkel, C., Yedidi, R. S.* Comparative in silico inter-spin distance analysis of IDSL spin labels modeled on lysozyme mutants against experimentally determined DEER distance measurements. Springer LNCS, 2018. (*Corresponding author).

  5. Bandhyopadhyay, A., VanEps, N., Eger, B. T., Rauscher, S., Yedidi, R. S., Moroni, T., West, G. M., Robinson, K. A., Griffin, P. R., Mitchell, J. A., Ernst, O. P. A novel polar core and weakly fixed C-tail in squid arrestin provide new instight into interaction with rhodopsin. J Mol Biol., 430:4102-4118, 2018. (Related PDB ID: 6BK9).

  6. Aoki, M., Hayashi, H., Kalapala, V. R., Das, D., Higashi-Kuwata, N., Bulut, H., Aoki-Ogata, H., Takamatsu, Y., Yedidi, R. S., Davis, D. A., Hattori, S-I., Nishida, N., Hasegawa, K., Takamune, N., Nyalapatla, P. R., Osswald, H. L., Yarchoan, R., Misumi, S., Ghosh, A. K., Mitsuya, H. A Novel Protease Inhibitor Overcomes HIV-1 Resistance with Unprecedented Potency. eLife, ;6. pii: e28020. doi: 10.7554/eLife.28020, 2017. (Related PDB IDs: 5TYR and 5TYS).

  7. Amano, M., Salcedo-Gomez, P. M., Yedidi, R. S., Delino, N. S., Nakata, H., Nakamura, T., Kalapala, V. R., Ghosh, A. K., Mitsuya, H. GRL-09510, a unique bridged-Tp-THF derivative ligand-containing HIV-1 protease inhibitor, maintains its favorable antiviral activity against highly-drug-resistant HIV-1 variants in vitro. Nature Scientific Reports, 7(1):12235. doi: 10.1038/s41598-017-12052-9, 2017. (Related PDB ID: 5V4Y).

  8. Zhu, C. G., Wu, E., Sailer, C., Jando, J., Eisenkolb, I., Wang, X., Huang, L., Yedidi, R. S., Friesen, H., Enenkel, C. Scaffold proteins in the orchestration of proteasome granule organization during quiescence in yeast. Mol Biol Cell, 28:2479-2491, 2017.

  9. Yedidi, R. S., Wendler, P., Enenkel, C. AAA-ATPases in protein degradation. Front. Mol. Biosci. 4:42, doi: 10.3389/fmolb.2017.00042, 2017.

  10. Yedidi, R. S., Fatehi, A., Enenkel, C. Proteasome dynamics between proliferation and quiescence stages of Saccharomyces cerevisiae. Crit. Rev. Biochem. Mol. Biol. 51:497-512, 2016.

  11. Amano, M., Salcedo-Gomez, P. M., Zhao, R., Yedidi, R. S., Das, D., Haydar, B., Nicole, S. D., Reddy, S. V., Ghosh, A. K., Mitsuya, H. A modified P1 moiety enhances in vitro antiviral activity against various multi-drug-resistant HIV-1 variants and in vitro CNS penetration properties of a novel nonpeptidic protease inhibitor, GRL-10413. Antimicrob Agents Chemother., 60 (12):7046-7059, 2016. (Related PDB ID: 3KAO).

  12. Aoki, M., Hayashi, H., Yedidi, R. S., Martyr, C. D., Takamatsu, Y., Aoki-Ogata, H., Nakamura, T., Nakata, H., Das, D., Yamagata, Y., Ghosh, A. K., Mitsuya, H. C5-modified tetrahydropyrano-tetrahydrofuran-derived protease inhibitors (PIs) exert potent inhibition of the replication of HIV-1 variants highly resistant to various PIs, including darunavir. J Virol. 90: 2180-2194, 2015. (Related PDB IDs: 5COK, 5CON, 5COO and 5COP).

  13. Yedidi, R. S., Proteasa, G., Martin, P. D., Liu, Z., Vickrey, J. F., Kovari, I. A., Kovari, L. C. A multi-drug resistant HIV-1 protease is resistant to the dimerization inhibitory activity of TLF-PafF. J Mol Graph Model. 53: 105-111, 2014. (Related PDB ID: 4NKK).

  14. Yedidi, R. S., Garimella, H., Aoki, M., Aoki-Ogata, H., Desai, D. V., Chang, S. B., Davis, D. A., Fyvie, S. W., Kaufman, J. D., Smith, D. W., Das, D., Wingfield, P. T., Maeda, K., Ghosh, A. K., Mitsuya, H. A conserved hydrogen-bonding network of P2 bis-tetrahydrofuran-containing HIV-1 protease inhibitors (PIs) with protease active-site amino acid backbone aids in their activity against PI-resistant HIV. Antimicrob Agents Chemother, 58:3679-3688, 2014. (Related PDB IDs: 4NJS, 4NJT, 4NJU and 4NJV).

  15. Yedidi, R. S., Liu, Z., Kovari, I. A., Woster, P. M., Kovari, L. C. P1 and P1' para-fluoro phenyl groups show enhanced binding and favorable predicted pharmacological properties: structure – based virtual screening of extended lopinavir analogs against multidrug resistant HIV-1 protease. J Mol Graph Model. 47: 18-24, 2014.

  16. Yedidi, R. S., Maeda, K., Fyvie, W. S., Steffey, M., Davis, D. A., Palmer, I., Aoki, M., Kaufman, J. D., Stahl, S. J., Garimella, H., Das, D., Wingfield, P. T., Ghosh, A. K., Mitsuya, H. P2' benzene carboxylic acid moiety is associated with decrease in cellular uptake: evaluation of novel nonpeptidic HIV-1 protease inhibitors containing P2 bis-tetrahydrofuran moiety. Antimicrob. Agents Chemother. 57: 4920-4927, 2013. (Related PDB IDs: 4HLA, 4I8W and 4I8Z).

  17. Yedidi, R. S., Muhuhi, J. M., Liu, Z., Bencze, K. Z., Koupparis, K., O'Connor, C. E., Kovari, I. A., Spaller, M. R., Kovari, L. C. Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease. Biochem Biophys Res Commun. 438: 703-708, 2013.

  18. Liu, Z., Yedidi, R. S., Wang, Y., Dewdney, T. G., Reiter, S. J., Brunzelle, J. S., Kovari, I. A., Kovari, L. C. Crystallographic study of multi-drug resistant HIV-1 protease lopinavir complex: mechanism of drug recognition and resistance. Biochem Biophys Res Commun. 437: 199-204, 2013. (Related PDB ID: 4L1A).

  19. Liu, Z., Yedidi, R. S., Wang, Y., Dewdney, T. G., Reiter, S. J., Brunzelle, J. S., Kovari, I. A., Kovari, L. C. Insights into the mechanism of drug resistance: X-ray structure analysis of multi-drug resistant HIV-1 protease ritonavir complex. Biochem Biophys Res Commun. 431: 232-238, 2013. (Related PDB ID: 4EYR).

  20. Liu, Z., Wang, Y., Yedidi, R. S., Dewdney, T. G., Reiter, S. J., Brunzelle, J. S., Kovari, I. A., Kovari, L. C. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes. Biochem Biophys Res Commun. 430: 1022-1027, 2013.

  21. Yedidi, R. S.*, Liu, Z., Wang, Y., Brunzelle, J. S., Kovari, I. A., Woster, P. M., Kovari, L. C., Gupta, D. Crystal structures of multidrug-resistant HIV-1 protease in complex with two potent anti-malarial compounds. Biochem Biophys Res Commun. 421: 413-417, 2012. (Related PDB IDs: 3R0W and 3R0Y). (*Corresponding author).

  22. Liu, Z., Wang, Y., Yedidi, R. S., Brunzelle, J. S., Kovari, I. A., Sohi, J., Kamholz, J., Kovari, L. C. Crystal structure of the extracellular domain of human myelin protein zero. Proteins. 80: 307-313, 2012. (Related PDB ID: 3OAI).

  23. Yedidi, R. S., Proteasa, G., Martinez, J. L., Vickrey, J. F., Martin, P. D., Wawrzak, Z., Liu, Z., Kovari, I. A., Kovari, L. C. Contribution of the 80s loop of HIV-1 protease to the multidrug-resistance mechanism: crystallographic study of MDR769 HIV-1 protease variants. Acta Crystallogr D Biol Crystallogr. 67: 524-532, 2011. (Related PDB IDs: 3PJ6, 3OQD, 3OQA and 3OQ7).

  24. Ide, K., Aoki, M., Amano, M., Koh, Y., Yedidi, R. S., Das, D., Leschenko, S., Chapsal, B., Ghosh, A. K., Mitsuya, H. Novel HIV-1 protease inhibitors (PIs) containing a bicyclic P2 functional moiety, tetrahydropyrano-tetrahydrofuran, that are potent against multi-PI-resistant HIV-1 variants. Antimircrob. Agents Chemother. 55: 1717-1727, 2011.

  25. Gupta, D., Yedidi, R. S., Varghese, S., Kovari, L. C., Woster, P. M. Mechanism-based inhibitors of the aspartyl protease plasmepsin II as potential antimalarial agents. J. Med. Chem. 53: 4234-4247, 2010.

  26. Ge, Y., Dombkowski, A. A., LaFiura, K. M., Tatman, D., Yedidi, R. S., Stout, M. L., Buck, S. A., Massey, G., Becton, D. L., Weinstein, H. J., Ravindranath, Y., Matherly, L. H., Taub, J. W. Differential gene expression, GATA1 target genes, and the chemotherapy sensitivity of syndrome megakaryocytic leukemia. Blood. 107: 1570-1581, 2006.

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