Diego E. Kleiman and Diwakar Shukla*, Active Learning of the Conformational Ensemble of Proteins using Maximum Entropy VAMPNets. bioRxiv, 2023. doi:10.1101/2023.01.12.523801.
Briana L Sobecks, Jiming Chen and Diwakar Shukla*, Mechanistic Basis for Enhanced Strigolactone Sensitivity in KAI2 Triple Mutant. bioRxiv, 2023. doi: 10.1101/2023.01.18.524622.
Austin T. Weigle and Diwakar Shukla*, AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition. bioRxiv, 2022, doi: 10.1101/2022.10.12.511964.
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Soumajit Dutta and Diwakar Shukla*, Distinct Activation Mechanisms Regulate Subtype Selectivity of Cannabinoid Receptors. bioRxiv, 2022. doi: 10.1101/2022.09.27.509760.
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Balaji Selvam#, Jiangyan Feng# and Diwakar Shukla*, Atomistic Insights Into The Mechanism of Dual Affinity Switching In Plant Nitrate Transporter NRT1.1. bioRxiv, 2022. doi: 10.1101/2022.10.17.512638.
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Anaira Román Santiago, Song Yin, Johannes Elbert, Jiho Lee, Diwakar Shukla, and Xiao Su*, Imparting selective fluorophilic interactions in redox copolymers for the electrochemically mediated capture of short-chain perfluoroalkyl substances. Journal of American Chemical Society, In press, 2023.
Prateek Bansal, Soumajit Dutta and Diwakar Shukla*, Activation Mechanism of the Human Smoothened Receptor. Biophysical Journal, In press, 2023.
Matthew C. Chan, Kui K. Chan, Erik Procko and Diwakar Shukla*, Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. Journal of Physical Chemistry B, In press, 2023.
Jiming Chen and Diwakar Shukla*, Effect of Histidine Covalent Modification on Strigolactone Receptor Activation and Selectivity. Biophysical Journal, In press, 2023.
Shriyaa Mittal, Soumajit Dutta and Diwakar Shukla*, Reconciling Membrane Protein Simulations with Experimental DEER Spectroscopy Data. Physical Chemistry Chemical Physics, In press, 2023.
Matthew Chan and Diwakar Shukla*, The Effects of N-linked Glycosylation on SLC6 Transporters. Journal of Chemical Information and Modeling, In press, 2023.
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Michael I. Jacobs, Prateek Bansal, Diwakar Shukla, and Charles M. Schroeder*, Understanding Supramolecular Assembly of Supercharged Proteins, ACS Central Science, Volume 8, Issue 9, Pages 1350–1361, 2022.
Matthew C Chan, Balaji Selvam, Heather J Young, Erik Procko and Diwakar Shukla*, The substrate import mechanism of the human serotonin transporter, Biophysical Journal, Volume 121, Issue 5, Pages 715-730, 2022.
Matthew C. Chan, Erik Procko, and Diwakar Shukla*, Structural Rearrangement of the Serotonin Transporter Intracellular Gate Induced by Thr276 Phosphorylation, ACS Chemical Neuroscience, Volume 13, Issue 7, Pages 933-945, 2022.
Jiming Chen, David C. Nelsonand Diwakar Shukla*, Activation Mechanism of Strigolactone Receptors and Its Impact on Ligand Selectivity between Host and Parasitic Plants, Journal of Chemical Information and Modeling, Volume 62, Issue 7, Pages 1712–1722, 2022.
Jesse R. Horne and Diwakar Shukla*, Recent Advances in Machine Learning Variant Effect Prediction Tools for Protein Engineering, Industrial & Engineering Chemistry Research, Volume 61, Issue 19, Pages 6235–6245, 2022.
Lianghui Zhang, Soumajit Dutta, Shiqin Xiong, Matthew Chan, Kui K Chan, Timothy M Fan, Keith L Bailey, Matthew Lindeblad, Laura M Cooper, Lijun Rong, Anthony F Gugliuzza, Diwakar Shukla, Erik Procko, Jalees Rehman, Asrar B Malik, Mechanistic origin of partial agonism of tetrahydrocannabinol for cannabinoid receptors, Nature Chemical Biology, Volume 18, Issue 3, Pages 342-351, 2022.
Soumajit Dutta, Balaji Selvam, Aditi Das, Diwakar Shukla*, Mechanistic origin of partial agonism of tetrahydrocannabinol for cannabinoid receptors, Journal of Biological Chemistry, Volume 298, Issue 4, Article number 101764, 2022.
Kyung Sun Park, Zhengyuan Xue, Bijal B. Patel, Hyosung An, Justin J. Kwok, Prapti Kafle, Qian Chen, Diwakar Shukla and Ying Diao*, Chiral emergence in multistep hierarchical assembly of achiral conjugated polymers, Nature Communications, Volume 13, Article number 2738, 2022.
Archit Kumar Vasan, Nandan Haloi, Rebecca Joy Ulrich, Mary Elizabeth Metcalf, Po-Chao Wen, William W Metcalf, Paul J Hergenrother, Diwakar Shukla and Emad Tajkhorshid*, Role of internal loop dynamics in antibiotic permeability of outer membrane porins, Proceedings of the National Academy of Sciences USA, Volume 119, Issue 8, Article number e2117009119, 2022.
Corina N D’Alessandro-Gabazza, Taro Yasuma, Tetsu Kobayashi, Masaaki Toda, Ahmed M Abdel-Hamid, Hajime Fujimoto, Osamu Hataji, Hiroki Nakahara, Atsuro Takeshita, Kota Nishihama, Tomohito Okano, Haruko Saiki, Yuko Okano, Atsushi Tomaru, Valeria Fridman D’Alessandro, Miyako Shiraishi, Akira Mizoguchi, Ryoichi Ono, Junpei Ohtsuka, Masayuki Fukumura, Tetsuya Nosaka, Xuenan Mi, Diwakar Shukla, Kensuke Kataoka, Yasuhiro Kondoh, Masaki Hirose, Toru Arai, Yoshikazu Inoue, Yutaka Yano, Roderick I Mackie, Isaac Cann, Esteban C Gabazza. Inhibition of lung microbiota-derived proapoptotic peptides ameliorates acute exacerbation of pulmonary fibrosis, Nature Communications, Volume 13, Issue 1, Article number 1558, 2022.
Soumajit Dutta, Balaji Selvam and Diwakar Shukla*, Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid Receptors, ACS Chemical Neuroscience, Volume 13, Issue 3, Pages 379-389, 2022.
Diego E Kleiman and Diwakar Shukla*, Multiagent reinforcement learning-based adaptive sampling for conformational dynamics of proteins, Journal of Chemical Theory and Computation, Volume 18, Issue 9, Pages 5422-5434, 2022.
Xuenan Mi and Diwakar Shukla*, Predicting the Activities of Drug Excipients on Biological Targets using One-Shot Learning, Journal of Physical Chemistry B, Volume 126, Issue 7, Pages 1492–1503, 2022.
Austin T Weigle, Jiangyan Feng and Diwakar Shukla*, Thirty years of molecular dynamics simulations on post-translational modifications of proteins, Physical Chemistry Chemical Physics, Volume 24, Pages 26371-26397, 2022.
Chuankai Zhao and Diwakar Shukla*, Molecular basis of the activation and dissociation of dimeric PYL2 receptor in abscisic acid signaling, Physical Chemistry Chemical Physics, Volume 24, Issue 2, Pages 724-734, 2022.
Xueyi Xue, Jiang Wang, Diwakar Shukla, Lily S. Cheung, and Li-Qing Chen, When SWEETs Turn Tweens: Updates and Perspectives, Annual Review of Plant Biology, Vol. 73, Issue 1, Pages 379-403, 2022.
Lars H Kruse, Austin T Weigle, Mohammad Irfan, Jesús Martínez‐Gómez, Jason D Chobirko, Jason E Schaffer, Alexandra A Bennett, Chelsea D Specht, Joseph M Jez, Diwakar Shukla, Gaurav D Moghe*, Orthology‐based analysis helps map evolutionary diversification and predict substrate class use of BAHD acyltransferases, The Plant Journal, Volume 111, Issue 5, Pages 1453-1468, 2022.
Briana L Sobecks, Jiming Chen and Diwakar Shukla*, Dual Role of Strigolactone Receptor Signaling Partner in Inhibiting Substrate Hydrolysis, Journal of Physical Chemistry B, Volume 126, Issue 11, Pages 2188-2195, 2022.
Jiming Chen and Diwakar Shukla*, Integration of machine learning with computational structural biology of plants, Biochemical Journal, Volume 479, Issue 8, Pages 921-928, 2022.
Diwakar Shukla#, Curtiss P. Schneider# and Bernhardt L. Trout*. Complex interactions between molecular ions in solution and their effect on protein stability. Journal of the American Chemical Society, Volume 133, Issue 46, Pages 18713-18718, 2011.
Diwakar Shukla and Bernhardt L. Trout*. Interaction of arginine with proteins and the mechanism by which it inhibits aggregation, Journal of Physical Chemistry B, Volume 114, Issue 42, Pages 13426-13438, 2010.
Diwakar Shukla, Chetan Shinde and Bernhardt L. Trout*. Molecular computations of preferential interaction coefficients of proteins, Journal of Physical Chemistry B, Volume 113, Issue 37, Pages 12546-12554, 2009.
Diwakar Shukla, Abhijeet A. Joshi and Anurag Mehra*. Modeling of formation of nanoparticles in reverse micellar systems: Ostwald ripening of silver halide particles, Langmuir, Volume 25, Issue 6, Pages 3786-3793, 2009.