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Fundamental and Computational Sciences Directorate

Staff information

Neeraj Kumar

Computational Biology
Data Scientist
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-18
Richland, WA 99352

PNNL Publications


  • Clyde A., S. Galanie, D.W. Kneller, H. Ma, Y. Babuji, B. Blaiszik, and A. Brace, et al. 2022. "High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor." Journal of Chemical Information and Modeling 62, no. 1:116-128. PNNL-SA-161210. doi:10.1021/acs.jcim.1c00851
  • Kim H., D.G. Hauner, J.A. Laureanti, A. Kruel, S. Raugei, and N. Kumar. 2022. "Mechanistic Investigation of SARS-CoV-2 Main Protease to Accelerate Design of Covalent Inhibitors." Scientific Reports 12, no. 1:Art. No. 21037. PNNL-SA-170467. doi:10.1038/s41598-022-23570-6
  • Knutson C.R., M.S. Bontha, J.A. Bilbrey, and N. Kumar. 2022. "Decoding the Protein-ligand Interactions Using Parallel Graph Neural Networks." Scientific Reports 12. PNNL-SA-166075. doi:10.1038/s41598-022-10418-2


  • Alexander F.J., J.A. Ang, J.A. Bilbrey, J. Balewski, T. Casey, R. Chard, and J. Choi, et al. 2021. "Co-design Center for Exascale Machine Learning Technologies (ExaLearn)." The International Journal of High Performance Computing Applications 35, no. 6:598-616. PNNL-SA-156070. doi:10.1177/10943420211029302
  • Choi R., M. Zhou, R. Shek, J.W. Wilson, L. Tillery, J.C. Craig, and I.A. Salukhe, et al. 2021. "High-throughput screening of the ReFRAME, Pandemic Box, and COVID Box drug repurposing libraries against SARS-CoV-2 nsp15 endoribonuclease to identify small-molecule inhibitors of viral activity." PLoS One 16, no. 4:e0250019. PNNL-SA-159108. doi:10.1371/journal.pone.0250019
  • Joshi R., A.D. McNaughton, D.G. Thomas, C. Henry, S. Canon, L. McCue, and N. Kumar. 2021. "Quantum Mechanical Methods Predict Accurate Thermodynamics of Biochemical Reactions." ACS Omega 6, no. 14:9948-9959. PNNL-SA-157024. doi:10.1021/acsomega.1c00997
  • Joshi R., and N. Kumar. 2021. "Artificial Intelligence for Autonomous Molecular Design: A Perspective." Molecules 26, no. 22:Art. No. 6761. PNNL-SA-159775. doi:10.3390/molecules26226761
  • Joshi R., N. Gebauer, M.S. Bontha, M. Khazaieli, R. James, B. Brown, and N. Kumar. 2021. "3D-Scaffold: Deep Learning Framework to Generate 3D Coordinates of Drug-like Molecules with Desired Scaffolds." Journal of Physical Chemistry B 125, no. 44:12166-12176. PNNL-SA-162972. doi:10.1021/acs.jpcb.1c06437
  • Matlock M., M. Hoffman, N. Dang, D. Folmsbee, L. Langkamp, G.R. Hutchison, and N. Kumar, et al. 2021. "Deep Learning Coordinate-Free Quantum Chemistry." Journal of Physical Chemistry A 125, no. 40:8978-8986. PNNL-SA-146299. doi:10.1021/acs.jpca.1c04462
  • Moses I., R. Joshi, B. Ozdemir, N. Kumar, J. Eickholt, and V. Barone. 2021. "Machine Learning Screening of Metal-ion Battery Electrode Materials." ACS Applied Materials & Interfaces 13, no. 45:53355-53362. PNNL-SA-160595. doi:10.1021/acsami.1c04627
  • Siriwardane E., R. Joshi, N. Kumar, and D. Cakir. 2021. "Revealing the Formation Energy-Exfoliation Energy-Structure Correlation of MAB Phases Using Machine Learning and DFT." ACS Applied Materials & Interfaces 12, no. 26:29424-29431. PNNL-SA-151212. doi:10.1021/acsami.0c03536


  • Artz J.H., O. Zadvornyy, D.W. Mulder, S.M. Keable, A.E. Cohen, M.W. Ratzloff, and S. Williams, et al. 2020. "Tuning catalytic bias of hydrogen gas producing hydrogenases." Journal of the American Chemical Society 142, no. 3:1227-1235. PNNL-SA-140081. doi:10.1021/jacs.9b08756


  • Kumar N., D. Butcher, and P.M. Kozlowski. 2019. "Reductive Co-C Bond Cleavage in B12-Dependent Methylmalonyl CoA Mutase: Mechanistic Implications." Journal of Physical Chemistry B 123, no. 10:2210-2216. PNNL-SA-138248. doi:10.1021/acs.jpcb.8b10820
  • Kumar N., J.M. Darmon, C.J. Weiss, M.L. Helm, S. Raugei, and R.M. Bullock. 2019. "Outer Coordination Sphere Proton Relay Base and Proximity Effects on Hydrogen Oxidation with Iron Electrocatalysts." Organometallics 38, no. 6:1391-1396. PNNL-SA-139298. doi:10.1021/acs.organomet.8b00805
  • Pegis M.L., D.J. Martin, C.F. Wise, A.C. Brezny, S. Johnson, L.E. Johnson, and N. Kumar, et al. 2019. "Mechanism of Catalytic O2 Reduction by Iron Tetraphenylporphyrin." Journal of the American Chemical Society 141, no. 20:8315-8326. PNNL-SA-141930. doi:10.1021/jacs.9b02640


  • Cannon W.R., J.D. Zucker, D.J. Baxter, N. Kumar, S.E. Baker, J. Hurley, and J.C. Dunlap. 2018. "Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation using Maximum Entropy-based Simulations with Application to Central Metabolism of Neurospora crassa." Processes 6, no. 6:Article No. 63. PNNL-SA-134563. doi:10.3390/pr6060063
  • Hurley J.M., M.S. Jankowski, H. De Los Santos, A.M. Crowell, S. Fordyce, J.D. Zucker, and N. Kumar, et al. 2018. "Circadian proteomic analysis uncovers mechanisms of post-transcriptional regulation in metabolic pathways." Cell Systems 7, no. 6:613-626. PNNL-SA-138421. doi:10.1016/j.cels.2018.10.014


  • Cardenas A.J., B. Ginovska-Pangovska, N. Kumar, J. Hou, S. Raugei, M.L. Helm, and A.M. Appel, et al. 2016. "Controlling Proton Delivery with Catalyst Structural Dynamics." Angewandte Chemie International Edition 55, no. 43:13509-13513. PNNL-SA-115082. doi:10.1002/anie.201607460
  • Pegis M.L., B.A. McKeown, N. Kumar, K. Lang, D.J. Wasylenko, P. Zhang, and S. Raugei, et al. 2016. "Homogenous Electrocatalytic Oxiygen Reduction Rates Correlate with Reaction Overpotential in Acidic Organic Solutions." ACS Central Science 2, no. 11:850-856. PNNL-SA-117180. doi:10.1021/acscentsci.6b00261


  • Darmon J.M., N. Kumar, E. Hulley, C.J. Weiss, S. Raugei, R.M. Bullock, and M.L. Helm. 2015. "Increasing the Rate of Hydrogen Oxidation without Increasing the Overpotential: A Bio-Inspired Iron Molecular Electrocatalyst with an Outer Coordination Sphere Proton Relay." Chemical Science 6, no. 5:2737-2745. PNNL-SA-105708. doi:10.1039/C5SC00398A
  • Hulley E., N. Kumar, S. Raugei, and R.M. Bullock. 2015. "Manganese-Based Molecular Electrocatalysts for Oxidation of Hydrogen." ACS Catalysis 5, no. 11:6838-6847. PNNL-SA-112291. doi:10.1021/acscatal.5b01751


  • Kumar N., D.M. Camaioni, M. Dupuis, S. Raugei, and A.M. Appel. 2014. "Mechanistic Insights into Hydride Transfer for Catalytic Hydrogenation of CO2 with Cobalt Complexes." Dalton Transactions 43, no. 31:11803-11806. PNNL-SA-101141. doi:10.1039/c4dt01551g

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