Publication in progress

• Rupesh Agarwal, Lioudmila V Loukachevitch, Barbara A Bensing, Hai Yu, Stefan Ruhl, Xi Chen, Paul M Sullam, Jeremy C. Smith, TM Iverson. "Mechanism of promiscuous binding to human and animal sialoglycan receptors by bacterial Siglec-like adhesins"

• Rupesh Agarwal, Barbara A. Bensing, Tina M. Iverson, Jeremy C. Smith. "Precise orientation of bacterial adhesin is critical for host adherence"

• Jens Glaser, David Rogers, Sara Delgaldo, Rupesh Agarwal, Rajitha Tatikonda, Stephanie Galanie, Micholas Dean Smith, John Eblen, Josh V. Vermaas, Ada Sedova, Swen Boehm, Matthew Baker, Isabella Daidone, Jeremy C. Smith."Targeting SARS CoV-2 non-structural proteins using billion-compound virtual screens"

Published

• Rupesh Agarwal, Ruisong Ye, Micholas Dean Smith, Jeremy C. Smith, and Leigh D. Quarles, Min Pi. "Osteocalcin binds to a GPRC6A Venus fly trap allosteric site to positively modulate GPRC6A signaling." FASEB BioAdvances (2024).

• Min Pi, Rupesh Agarwal, Micholas Dean Smith, Jeremy C Smith, Leigh D Quarles. "GPRC6A is a Potential Therapeutic Target for Metformin Regulation of Glucose Homeostasis in Mice." bioRxiv (2024).

• Rupesh Agarwal, Pawat Pattarawat, Michael R. Duff, Hwa-Chain Robert Wang, Jerome Baudry, and Jeremy C. Smith. "Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors." Pharmaceuticals (2024)

• Wang, Y.Y., Wang, Y., Liang, L., Smith, M.D., Meng, X., Pu, Y., Mazarei, M., Rupesh Agarwal, Rukmani, S.J., Davison, B.H. and Ragauskas, A.J., "Characterization and molecular simulation of lignin in Cyrene pretreatment of switchgrass." Green Chemistry (2024)

• Rupesh Agarwal, Rajitha Rajeshwar T. and Jeremy C. Smith. "Comparative Assessment of Pose Prediction Accuracy in RNA–Ligand Docking." Journal of Chemical Information and Modeling (2023).

• Rupesh Agarwal, Jeremy C. Smith. " Speed vs accuracy: Effect on ligand pose accuracy of varying box size and exhaustiveness in AutoDock Vina" Molecular Informatics 42.2 (2023): 2200188

• Beamer, Zachary G., Pratyush Routray, Rupesh Agarwal, Tian Li, Katey M. Gibson, Katherine E. Ostrouchov, Jeremy C. Smith, and Daniel M. Roberts. "Differential Boric Acid and Water Transport in Type I and Type II Pores of Arabidopsis Nodulin 26-Intrinsic Protein." bioRxiv (2022).

• Bensing, Barbara A., Haley E. Stubbs, Rupesh Agarwal, Izumi Yamakawa, Kelvin Luong, Kemal Solakyildirim, Hai Yu et al. "Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation." Nature Communications 13, no. 1 (2022): 1-14.

• Glaser, Jens; Sedova, Ada; Galanie, Stephanie; Kneller, Daniel; Davidson, Russell; Maradzike, Elvis; Del Galdo, Sara; Labbé, Audrey; Hsu, Darren; Agarwal, Rupesh; Bykov, Dmytro; Tharrington, Arnold; Parks, Jerry; Smith, Dayle; Daidone, Isabella; Coates, Leighton; Kovalevsky, Andrey; Smith, Jeremy. "Hit expansion of a non-covalent SARS-CoV-2 main protease inhibitor ". ACS Pharmacology & Translational Science 

• Rogers, David M., Rupesh Agarwal, Josh V. Vermaas, Micholas Dean Smith, Rajitha T. Rajeshwar, Connor Cooper, Ada Sedova et al. "SARS-CoV2 billion-compound docking." Scientific Data 10, no. 1 (2023): 173.

• Ivette Perez, Sandra Berndt, Rupesh Agarwal, Manuel A Castro, Sergey A Vishnivetskiy, Jeremy C Smith, Charles R Sanders, Vsevolod V Gurevich, TM Iverson."A model for the signal initiation complex between arrestin-3 and the Src family kinase Fgr". Journal of Molecular Biology

• Jay A. Spencer, Tom Penfound, Michelle P. Aranha, Rupesh Agarwal, Jeremy C. Smith, James B. Dale , Jerome Baudry. "Streptococcus pyogenes Vaccine Design Strategy: Recurrent Neural Network Identification of Conserved M Protein Linear Epitopes". Vaccine

• Gupta, Madhulika, Khanh Ha, Rupesh Agarwal, Leigh Darryl Quarles, and Jeremy C. Smith. "Molecular dynamics analysis of the binding of human interleukin-6 with interleukin-6 α-receptor." Proteins: Structure, Function, and Bioinformatics 89, no. 2 (2021): 163-173.

• Rupesh Agarwal, Micholas D. Smith, Jeremy C. Smith. "Capturing deuteration effects in classical molecular dynamics simulations: Mixing behavior of tetrahydrofuran in aqueous solution". Journal of Chemical Theory and Computation, doi.org/10.1021/acs.jctc.9b01138 (2020)

• Rupesh Agarwal, Utsab R. Shrestha, Loukas Petridis, Xiang-Qiang Chu, Jeremy C. Smith. "Mesophilic pyrophosphatase function at high temperature: a molecular dynamics simulation study". Biophysical Journal doi.org/10.1016/j.bpj.2020.05.021 (2020)

• Rupesh Agarwal, Barbara A. Bensing, Jerome Baudry, Tina M Iverson, Jeremy C. Smith,. "Structure based virtual screening identifies novel competitive inhibitors for the sialoglycan binding protein Hsa". Biochemical Journal doi.org/10.1042/BCJ20200332 (2020)

• Aranha, Michelle P., Thomas A. Penfound, Jay A. Spencer, Rupesh Agarwal, Jerome Baudry, James B. Dale, and Jeremy C. Smith. "Structure-based group A streptococcal vaccine design: Helical wheel homology predicts antibody cross-reactivity among streptococcal M protein-derived peptides." Journal of Biological Chemistry 295, no. 12 (2020): 3826-3836

• LeGrand, Scott, Aaron Scheinberg, Andreas F. Tillack, Mathialakan Thavappiragasam, Josh V. Vermaas, Rupesh Agarwal, Jeff Larkin et al. "GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research." In Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, pp. 1-10. 2020.

• Acharya, Atanu, Rupesh Agarwal, M. B. Baker, Jerome Baudry, Debsindhu Bhowmik, Swen Boehm, K. G. Byler et al. "Supercomputer-based ensemble docking drug discovery pipeline with application to COVID-19." Journal of chemical information and modeling (2020).

• Sen, Sanjukta, Rupesh Agarwal, Prafulla Ambulkar, Indira Hinduja, Kusum Zaveri, Jyotsna Gokral, Asoke Pal, and Deepak Modi. "Deletion of GOLGA2P3Y but not GOLGA2P2Y is a risk factor for oligozoospermia." Reproductive biomedicine online 32, no. 2 (2016): 218-224.