127. Haiyang Cui, Yufeng Su, Tanner J. Dean, Tianhao Yu, Jian Peng, Diwakar Shukla* and H. Zhao*, EZSpecficity: Decoding Enzyme Substrate Specificity with Cross Attention-enhanced Graph Neural Networks. In review, 2024.
126. Joseph D. Clark, Xuenan Mi, Douglas A. Mitchell and Diwakar Shukla*, Substrate Prediction for RiPP Biosynthetic Enzymes via Masked Language Modeling and Transfer Learning. arXiv, 2024. doi: 10.48550/arXiv.2402.15181
Publication Link
125. Balaji Selvam, Nicole Chiang and Diwakar Shukla*. Energetics of substrate transport and proton movement in Oligopeptide transporter, PepTSo. biorXiv, 2024. doi: 10.1101/2024.05.01.592129
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124. Zahra Shamsi and Diwakar Shukla*, Billion-years old proteins show the importance of N-lobe orientation in Imatinib-kinase selectivity. bioRxiv, 2023. doi: 10.48550/arXiv.2303.15586
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123. Austin T. Weigle and Diwakar Shukla*. Interplay between phosphorylation and oligomerization tunes the conformational ensemble of SWEET transporters. bioRxiv, 2024. doi: 10.1101/2024.06.12.598708
Publication Link
122. Krishna K. Narayanan, Austin T. Weigle, Lingyun Xu, Xuenan Mi, Li-Qing Chen, Erik Procko and Diwakar Shukla*. Sequence to function constraints for plant SWEET transporter using deep mutational scanning. bioRxiv, 2024. doi: 10.1101/2024.06.28.601307
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121. Balaji Selvam, Arnav Paul, Ya-Chi Yu, Li-Qing Chen and Diwakar Shukla*, SWEET family transporters act as water conducting carrier proteins in plants. bioRxiv, 2024. doi: 10.1101/2024.06.23.600272
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120. 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.
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119. Chuankai Zhao and Diwakar Shukla*, Structural Basis for Negative Regulation of ABA Signaling by ROP11 GTPase. bioRxiv, 2022. doi: 10.1101/2020.05.20.107185.
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118. 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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117. Jiming Chen and Diwakar Shukla*, Multiple modes of substrate hydrolysis-induced covalent modification of strigolactone receptors. bioRxiv, 2022, doi: 10.1101/2022.04. 22.489200.
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116. Matthew C. Chan, Yazeed Alfawaz and Diwakar Shukla*. Molecular Mechanism of Substrate Transport and Dynamics of the Cyanobacterial Bicarbonate Transporter BicA. bioRxiv, 2022, doi: 10.1101/2022.06.08.495363.
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115. Heather J. Young, Matthew C. Chan, Balaji Selvam, Steven K. Szymanski, Diwakar Shukla* and Erik Procko*. Deep Mutagenesis of a Transporter for Uptake of a Non-Native Substrate Identifies Conformationally Dynamic Regions. bioRxiv, 2021. doi: 10.1101/2021.04.19.440442.
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114. Kihong Kim, Prateek D. Bansal and Diwakar Shukla*. Binding Position Dependent Modulation of Smoothened Activity by Cyclopamine. Communications Biology, In press, 2024.
113. Soumajit Dutta and Diwakar Shukla*, Characterization of binding kinetics and intracellular signaling of new psychoactive substances targeting cannabinoid receptor using transition-based reweighting method. elife, In press, 2024. doi: 10.7554/eLife.98798.1
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112. Susanna E. Barrett, Song Yin, Peter Jordan , John Brunson , Jessica Gordon-Nunez , Gabriella Costa Machado da Cruz , Christopher Rosario , Bethany Okada , Kelsey Anderson , Thomas Pires , Ruoyang Wang, Diwakar Shukla, Mark Burk, Douglas A. Mitchell*. Substrate interactions guide cyclase engineering and lasso peptide diversification. Nature Chemical Biology, In press, 2024.
111. Austin T. Weigle and Diwakar Shukla*, The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition. Communications Biology, Volume 7, Article number: 764, 2024.
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110. Maria Daniela Torres-Rodriguez, Soon Goo Lee, Swarup Roy Choudhury, Rabindranath Paul, Balaji Selvam, Diwakar Shukla, Joseph M. Jez and Sona Pandey, Structure-function analysis of plant G-protein regulatory mechanisms identifies key Gα-RGS protein interactions. Journal of Biological Chemistry, Volume 300, Issue 5, 107252, 2024.
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109. Song Yin, Xuenan Mi and Diwakar Shukla*, Leveraging Machine Learning Models for Peptide-Protein Interaction Prediction, RSC Chemical Biology, Volume 5, Pages 401-417, 2024.
Invited article
Publication Link
108. Arnav Paul and Diwakar Shukla*, Oligomerization of monoamine transporters. In: Harris, J.R., Marles-Wright, J. (eds) Macromolecular Protein Complexes: Part V, Subcellular Biochemistry, Volume 104, Springer, Cham., 2024.
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107. Anh T. P. Nguyen, Austin T. Weigle and Diwakar Shukla*, Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition. Nature Communications, Volume 15, Article number: 1848, 2024.
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106. Jiming Chen, Tanner J. Dean and Diwakar Shukla*. Contribution of Signaling Partner Association to Strigolactone Receptor Selectivity. Journal of Physical Chemistry B, Volume 128, Issue 32024.
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105. Sarah E. Lindley, Yiyang Lu and Diwakar Shukla*, The Experimentalist’s Guide to Machine Learning for Small Molecule Design. ACS Applied Bio Materials, Volume 7, Issue 2, Pages 657–684, 2024
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104. Chuankai Zhao, Diego E. Kleiman and Diwakar Shukla*, Resolving binding pathways and solvation thermodynamics of plant hormone receptors. Journal of Biological Chemistry, Volume 299, Issue 12, Article 105456, 2023.
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103. Diego E Kleiman, Hassan Nadeem and Diwakar Shukla*, Adaptive Sampling Methods for Molecular Dynamics in the Era of Machine Learning. Journal of Physical Chemistry B, Volume 127, Issue 50, 2023.
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Invited Perspective
102. Krishna Narayanan, Moushimi Amaya, Natalie Tsang, Randy Yin, Alka Jays, Christopher C Broder, Diwakar Shukla, Erik Procko*, The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins. Journal of Virology, Volume 97, Issue 11, e00621-23, 2023.
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101. Prateek Bansal, Soumajit Dutta and Diwakar Shukla*, Activation Mechanism of the Human Smoothened Receptor. Biophysical Journal, Volume 122, Issue 7, Pages 1400-1413, 2023.
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100. 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, Volume 145, Issue 17, 2023.
Publication Link
Highlighted on Journal Cover and News
99. Matthew Chan and Diwakar Shukla*, The Effects of N-linked Glycosylation on SLC6 Transporters. Journal of Chemical Information and Modeling, Volume 63, Issue 92023.
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98. Diego E. Kleiman and Diwakar Shukla*, Active Learning of the Conformational Ensemble of Proteins using Maximum Entropy VAMPNets. Journal of Chemical Theory and Computation, Volume 19, Issue 14, 2023.
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97. Soumajit Dutta and Diwakar Shukla*, Distinct Activation Mechanisms Regulate Subtype Selectivity of Cannabinoid Receptors. Communications Biology, Volume 6, Article number: 4852022, 2023.
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96. Xuenan Mi, Emily K. Desormeaux, Tung T. Le, Wilfred A. van der Donk and Diwakar Shukla*, Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization. Chemical Science, Volume 14, Pages 6904-6914, 2023.
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95. 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, Volume 127, Issue 9, 2023.
Publication Link
94. Jiming Chen and Diwakar Shukla*, Effect of Histidine Covalent Modification on Strigolactone Receptor Activation and Selectivity. Biophysical Journal, Volume 122, Issue 7, Pages 1219-1228, 2023.
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93. Shriyaa Mittal, Soumajit Dutta and Diwakar Shukla*, Reconciling Membrane Protein Simulations with Experimental DEER Spectroscopy Data. Physical Chemistry Chemical Physics, Volume 25, Issue 8, Pages 6253-6262, 2023.
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92. 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.
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91. 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.
Publication Link
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90. 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.
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89. Jiming Chen, David C. Nelson and 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 , 2022.
Publication Link
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88. 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.
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87. 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.
Publication Link
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86. 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.
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Highlighted in ASBMB Today.
85. 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.
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84. 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.
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83. 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.
Publication Link
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82. 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.
Publication Link
81. 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.
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80. 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.
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79. 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.
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Perspective article
78. 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.
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77. 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.
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76. 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.
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75. 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.
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74. 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.
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73. Austin Tyler Weigle, Matthew Carr, Diwakar Shukla*, Impact of increased membrane realism on conformational sampling of proteins. Journal of Chemical Theory and Computation, Volume 61, Issue 10, Pages 4827–4831, 2021.
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72. Daniel T Bregante, Matthew C Chan, Jun Zhi Tan, E Zeynep Ayla, Christopher P Nicholas, Diwakar Shukla, David W Flaherty*, The shape of water in zeolites and its impact on epoxidation catalysis. Nature Catalysis, Volume 4, Issue 9, Pages 797-808, 2021.
Publication link
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71. Gabriel V Pereira, Ahmed M Abdel-Hamid, Soumajit Dutta, Corina N D’Alessandro-Gabazza, Daniel Wefers, Jacob A Farris, Shiv Bajaj, Zdzislaw Wawrzak, Haruyuki Atomi, Roderick I Mackie, Esteban C Gabazza, Diwakar Shukla, Nicole M Koropatkin, Isaac Cann*, Degradation of complex arabinoxylans by human colonic Bacteroidetes. Nature Communications, Volume 12, Article 459, 2021.
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70. Raylin Chen, Jiangyan Feng, Jemin Jeon, Thomas Sheehan, Christian Rüttiger, Markus Gallei, Diwakar Shukla, Xiao Su*, Structure and Potential‐Dependent Selectivity in Redox‐Metallopolymers: Electrochemically Mediated Multicomponent Metal Separations. Advanced Functional Materials, Volume 31, Issue 15, Article 2009307, 2021.
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69. Jiangyan Feng, Balaji Selvam and Diwakar Shukla*, How do antiporters exchange substrates across the cell membrane? An atomic-level description of the complete exchange cycle in NarK. Structure, Volume 29, Issue 8, Pages 922-933. e3, 2021.
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68. Jiming Chen, Alexandra White, David C Nelson and Diwakar Shukla*, Role of substrate recognition in modulating strigolactone receptor selectivity in witchweed. Journal of Biological Chemistry, Volume 297, Issue 4, Article 101092, 2021.
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67. Nurzhan Kuanyshev, Anshu Deewan, Sujit Sadashiv Jagtap, Jingjing Liu, Balaji Selvam, Li‐Qing Chen, Diwakar Shukla*, Christopher V Rao*, Yong‐Su Ji*, Structure and Potential‐Dependent Selectivity in Redox‐Metallopolymers: Electrochemically Mediated Multicomponent Metal Separations. Biotechnology Journal, Volume 16, Issue 11, Article 2100238, 2021.
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66. Matthew C. Chan and Diwakar Shukla*, Markov state modeling of membrane transport protein. Journal of Structural Biology, Volume 213, Issue 4, Article 107800, 2021.
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65. Alexander S. Moffet and Diwakar Shukla*, Structural consequences of multisite phosphorylation in the BAK1 kinase domain, Biophysical Journal, Volume 118, Issue 3, Pages 698-707, 2020.
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64. Zahra Shamsi, Matthew Chan and Diwakar Shukla*, TLmutation: predicting the effects of mutations using transfer learning. The Journal of Physical Chemistry B, Volume 124, Issue 19, Pages 3845-3854, 2020.
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63. Jiangyan Feng and Diwakar Shukla*, FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution. The Journal of Physical Chemistry B, Volume 124, Issue 18, Pages 3605-3615, 2020.
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62. Luke Cuculis, Chuankai Zhao, Zhanar Abil, Huimin Zhao, Diwakar Shukla, Charles M Schroeder*, Divalent cations promote TALE DNA-binding specificity, Nucleic Acids Research, Volume 48, Issue 3, Pages 1406-1422, 2020.
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61. Zahra Shamsi and Diwakar Shukla*, How does evolution design functional free energy landscapes of proteins? A case study on the emergence of regulation in the Cyclin Dependent Kinase family, Molecular Systems Design and Engineering, Volume 5, Issue 1, Pages 393-400, 2020.
Publication Link
Invited Article for Young Investigators in MSDE.
60. Jihye Park, Balaji Selvam, Keisuke Sanematsu, Noriatsu Shigemura, Diwakar Shukla, Erik Procko*, Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits, Journal of Biological Chemistry, Volume 294, Issue 13, Pages 4759-4774, 2019.
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59. Drishti Guin, Shriyaa Mittal, Brian Bozymski, Diwakar Shukla*, Martin Gruebele*, Dodine as a Kosmo-Chaotropic agent, The Journal of Physical Chemistry Letters, Volume 10, Issue 10, Pages 2600-2605, 2019.
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58. Balaji Selvam, Ya-Chi Yu, Li-Qing Chen and Diwakar Shukla*, Molecular basis of the glucose transport mechanism in plants, ACS Central Science, Volume 5, Issue 6, Pages 1085-1096, 2019.
Publication Link
56. Saurabh Shukla, Chuankai Zhao and Diwakar Shukla*, Dewetting controls plant hormone perception and initiation of drought resistance signaling, Structure, Volume 27, Issue 4, Pages692-702.e3, 2019.
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55. Kevin J Cheng, Balaji Selvam, Li-Qing Chen and Diwakar Shukla*, Distinct substrate transport mechanism identified in homologous sugar transporters, The Journal of Physical Chemistry B, Volume 123, Issue 40, Pages 8411-8418, 2019.
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54. Alexander S Moffett and Diwakar Shukla*, How do brassinosteroids activate their receptors?. BioRxiv, 2019, doi:10.1101/630640.
Publication Link
53. Faisal Aldukhi, Aniket Deb, Chuankai Zhao, Alexander S Moffett and Diwakar Shukla*, Molecular mechanism of brassinosteroid perception by the plant growth receptor BRI1. The Journal of Physical Chemistry B, Volume 124, Issue 2, Pages 355-365, 2019.
Publication Link
52. Erfan Mohammadi, Chuankai Zhao, Fengjiao Zhang, Ge Qu, Seok-Heon Jung, Qiujie Zhao, Christopher M Evans, Jin-Kyun Lee, Diwakar Shukla, Ying Diao*, Ion Gel Dynamic Templates for Large Modulation of Morphology and Charge Transport Properties of Solution-Coated Conjugated Polymer Thin Films. ACS Applied Material and Interfaces, Volume 11, Issue 25, Pages 22561-22574 2019.
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51. Balaji Selvam, Zahra Shamsi and Diwakar Shukla*, Universality of the sodium ion binding mechanism in class AG‐protein‐coupled receptors, Angewandte Chemie, Volume 12, Pages 3102-3107, 2018.
Publication Link
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50. Balaji Selvam, Shriyaa Mittal and Diwakar Shukla*, Free energy landscape of the complete transport cycle in a key bacterial transporter. ACS Central Science, Volume 4, Issue 9, Pages 1146-1154, 2018.
Publication Link
49. Alexander S Moffett and Diwakar Shukla*, Using molecular simulation to explore the nanoscale dynamics of the plant kinome. Biochemical Journal, Volume 475, Issue 5, Pages 905-921, 2018.
Publication Link
Invited Review Article
48. Chuankai Zhao and Diwakar Shukla*, SAXS-guided enhanced unbiased sampling for structure determination of proteins and complexes. Scientific Reports, Volume 8, Issue 1, Article 17748, 2018.
Publication Link
47. Qihua Chen, Jiangyan Feng, Shriyaa Mittal and Diwakar Shukla*, Automatic Feature Selection in Markov State Models Using Genetic Algorithm. Journal of Computational Science and Education, Volume 9, Issue 2, Pages 14-22, 2018.
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46. Shriyaa Mittal and Diwakar Shukla*, Maximizing kinetic information gain of Markov state models for optimal design of spectroscopy experiments. The Journal of Physical Chemistry B, Volume 122, Issue 48, Pages 10793-10805, 2018.
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45. Zahra Shamsi, Kevin J. Cheng and Diwakar Shukla*, Reinforcement learning based adaptive sampling: REAPing rewards by exploring protein conformational landscapes. The Journal of Physical Chemistry B, Volume 122, Issue 35, Pages 8386-8395, 2018.
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44. Shriyaa Mittal and Diwakar Shukla*, Recruiting machine learning methods for molecular simulations of proteins. Molecular Simulation, Volume 44, Issue 11, Pages 891-904, 2018.
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43. Jiangyan Feng and Diwakar Shukla*, Characterizing conformational dynamics of proteins using evolutionary couplings, The Journal of Physical Chemistry B, Volume 122, Issue 3, Pages 1017-1025, 2018.
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42. Shriyaa Mittal and Diwakar Shukla*, Predicting optimal deer label positions to study protein conformational heterogeneity, The Journal of Physical Chemistry B, Volume 121, Issue 42, Pages 9761-9770, 2017.
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41. Erfan Mohammadi, Chuankai Zhao, Yifei Meng, Ge Qu, Fengjiao Zhang, Xikang Zhao, Jianguo Mei, Jian-Min Zuo, Diwakar Shukla, Ying Diao*, Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films. Nature Communications, Volume 8, Article 16070, 2017.
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40. Alexander S Moffett, Kyle W Bender, Steven C Huber, Diwakar Shukla*, Allosteric control of a plant receptor kinase through S-glutathionylation. Biophysical Journal, Volume 113, Issue 11, Pages 2354-2363, 2017.
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39. Zahra Shamsi, Alexander S Moffett and Diwakar Shukla*, Enhanced unbiased sampling of protein dynamics using evolutionary coupling information, Scientific Reports, Volume 7, Article 12700, 2017.
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38. Alexander S Moffett and Diwakar Shukla*, On the transferability of time-lagged independent components between similar molecular dynamics systems, arXiv, 2017, doi: 10.48550/arXiv.1710.00443.
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37. Amy Marshall-Colon, Stephen P Long, Douglas K Allen, Gabrielle Allen, Daniel A Beard, Bedrich Benes, Susanne Von Caemmerer, AJ Christensen, Donna J Cox, John C Hart, Peter M Hirst, Kavya Kannan, Daniel S Katz, Jonathan P Lynch, Andrew J Millar, Balaji Panneerselvam, Nathan D Price, Przemyslaw Prusinkiewicz, David Raila, Rachel G Shekar, Stuti Shrivastava, Diwakar Shukla, Venkatraman Srinivasan, Mark Stitt, Matthew J Turk, Eberhard O Voit, Yu Wang, Xinyou Yin, Xin-Guang Zhu, Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform, Frontiers in plant science, Volume 8, Pages 786, 2017.
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Perspective Article
36. Saurabh Shukla, Zahra Shamsi, Alexander S Moffett, Balaji Selvam, Diwakar Shukla*, Application of hidden Markov models in biomolecular simulations, Hidden Markov Models: Methods and Protocols, Pages 29-41, 2017.
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35. Alexander S Moffett, Kyle W Bender, Steven C Huber, Diwakar Shukla*, Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases. Journal of Biological Chemistry, Volume 292, Issue 30, Pages 12643-12652, 2017.
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34. Yilin Meng, Diwakar Shukla, Vijay S Pande, Benoit Roux, Transition path theory analysis of c-Src kinase activation, Proceedings of National Academy of Sciences, Volume 113, Issue 33, Pages 9193-9198, 2016.
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33. Christian R Schwantes, Diwakar Shukla, Vijay S Pande, Markov state models and tICA reveal a nonnative folding nucleus in simulations of NuG2, Biophysical Journal, Volume 110, Issue 8, Pages 1716-1719, 2016.
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32. Diwakar Shukla, Ariana Peck, Vijay S Pande, Conformational heterogeneity of the calmodulin binding interface, Nature Communications, Volume 7, Article number: 10910, 2016.
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31. Lili X Peng, Morgan Lawrenz, Diwakar Shukla, Grace W Tang, Vijay S Pande, Russ B Altman, Application of new informatics tools for identifying allosteric lead ligands of the c-Src kinase, bioRxiv, 2016, doi:10.1101/038323.
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30. Dan Vanatta, Diwakar Shukla, Morgan Lawrenz, and Vijay S. Pande, A Network of Molecular-Switches Control the Activation of a Key Bacterial Signaling Protein. Nature Communications, Volume 6, Article number:7283, 2015.
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29. Jeffery K. Weber, Diwakar Shukla and Vijay S. Pande, Heat Dissipation Guides Activation of Signaling Proteins, Proceedings of the National Academy Sciences USA, Volume 557, Pages 551-572, 2015.
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28. Diwakar Shukla, Carlos X. Hernandez, Jeffery K. Weber and Vijay S. Pande, Markov State Models Provide Insights into Dynamic Modulation of Protein Function, Accounts of Chemical Research, Volume 48, Issue 2, Pages 414- 422, 2015.
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27. Morgan Lawrenz, Diwakar Shukla and Vijay S. Pande, Cloud-computing Approaches for Predicting Ligand Binding Poses and Pathways, Scientific Reports, Volume 5, Article number: 7918, 2015.
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26. Matthew Harrigan, Diwakar Shukla and Vijay S. Pande. Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics. Journal of Chemical Theory & Computation, Volume 11, Pages 1094-1101, 2015.
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25. Diwakar Shukla, Morgan Lawrenz and Vijay S. Pande, Elucidating ligand-modulated Conformational Landscape of GPCRs, Methods in Enzymology, Volume 557, Pages 551-572, 2015.
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24. Kai Kohlhoff*, Diwakar Shukla*, Morgan Lawrenz, Gregory R. Bowman, David E. Konerding, Dan Belov, Russ B. Altman and Vijay S. Pande, Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nature Chemistry, Volume 6, Pages 15-21, 2014. *Equal Contribution.
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Commentary about this article
23. Diwakar Shukla, Yilin Meng, Benoit Roux and Vijay S. Pande, Activation pathway of Src kinase reveals intermediate states as novel targets for drug design. Nature Communications, Volume 5, Article number: 3397, 2014.
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22. Lisa J. Lapidus, S. Acharya, C. Schwantes, L. Wu, Diwakar Shukla, M. King, S. J. DeCamp and Vijay S. Pande. Complex Pathways in Folding of Protein G Explored by Simulation and Experiment. Biophysical Journal, Volume 107, Issue 4, Pages 947-955, 2014.
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21. Mohammad M. Sultan, Gert Kiss, Diwakar Shukla and Vijay S. Pande, Automatic Order Parameters Selection In Markov State Models for Atomistic Understanding of Molecular Dynamics Data, Journal of Chemical Theory & Computation, Volume 10, Issue 12, Pages 5217-5223, 2014.
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20. Peter Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, Diwakar Shukla, T. Tye, M. Houston, T. Stich, C. Klein, M. R. Shirts, Vijay S. Pande, OpenMM 4.0: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. Journal of Chemical Theory & Computation, Volume 9, Issue 1, Pages 461-469, 2013.
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19. Thomas J. Lane, Diwakar Shukla, Kyle A. Beauchamp and Vijay S. Pande, To Milliseconds and Beyond: Challenges in the Simulation of Protein Folding. Current Opinion in Structural Biology, Volume 23, Issue 1, Pages 58- 65, 2013.
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18. Diwakar Shukla, and Bernhardt L. Trout*, Understanding the Role of Arginine and Citrate as Eluents in Affinity Chromatography, Developments in Biotechnology and Bioprocessing, ACS Symposium Series, Chapter 5, Pages 67-86, 2013.
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17. 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.
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16. Curtiss P. Schneider#, Diwakar Shukla# and Bernhardt L. Trout*. Effects of solute-solute interactions on protein stability studied using various counterions and dendrimers. PLoS One, Volume 6, Issue 11, Article number e27665, 2011.
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15. Diwakar Shukla and Bernhardt L. Trout*. Understanding the synergistic effect of arginine and glutamic acid mixtures on protein solubility. Journal of Physical Chemistry B, Volume 115, Issue 41, Pages 11831-11839, 2011.
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14. Diwakar Shukla#, Curtiss P. Schneider# and Bernhardt L. Trout*. Molecular level insight into intra-solvent interaction effects on protein stability and aggregation. Advanced Drug Delivery Reviews, Volume 63, Issue 13, Pages 1074-1085, 2011.
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13. Diwakar Shukla#, Curtiss P. Schneider# and Bernhardt L. Trout*. Effects of PAMAM dendrimer salt solutions on protein stability. Journal of Physical Chemistry Letters, Volume 2, Issue 14, Pages 1782-1788, 2011.
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12. Curtiss P. Schneider#, Diwakar Shukla# and Bernhardt L. Trout*. Arginine and the Hofmeister series: the role of ion–ion interactions in protein aggregation suppression. Journal of Physical Chemistry B, Volume 115, Issue 22, Pages 7447-7458, 2011.
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11. Diwakar Shukla, Laura Zamolo, Carlo Cavallotti and Bernhardt L. Trout*. Understanding the role of arginine as an eluent in affinity chromatography via molecular computations. Journal of Physical Chemistry B, Volume 115, Issue 11, Pages 2645-2654, 2011.
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10. Diwakar Shukla and Bernhardt L. Trout*. Preferential interaction coefficients of proteins in aqueous arginine solutions and their molecular origins. Journal of Physical Chemistry B, Volume 115, Issue 5, Pages 1243-1253, 2011.
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9. 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.
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8. 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.
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7. 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.
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6. Asaf Kleopas Sugih, Diwakar Shukla, H J Heeres and Anurag Mehra*. CaCO3 nanoparticle synthesis by carbonation of lime solution in microemulsion systems, Nanotechnology, Volume 18, Issue 3, Article number 035607, 2006.
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5. Diwakar Shukla and Anurag Mehra*. Modeling Shell Formation in Core-Shell Nanocrystals in Reverse Micelle Systems, Langmuir, Volume 22, Issue 23, Pages 9500–9506, 2006.
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4. Diwakar Shukla and Anurag Mehra*, Modeling of the Formation of Nanoparticles in Reverse Micellar Systems. Proceeding of the 17th International Congress of Chemical and Process Engineering, Prague, Czech Republic, 2006.
3. Ravi Jain, Diwakar Shukla and Anurag Mehra*. A Monte Carlo Model for the Formation of Core−Shell Nanocrystals in Reverse Micellar Systems, Industrial and Engineering Chemistry Research, Volume 45, Issue 7, Pages 2249–2254, 2006.
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2. Diwakar Shukla and Anurag Mehra*. A model for particle coagulation in reverse micelles with a size dependent coagulation rate, Nanotechnology, Volume 17, Issue 1, Pages 261–267, 2005.
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1. Ravi Jain, Diwakar Shukla and Anurag Mehra. Coagulation of nanoparticles in reverse micellar systems: A Monte Carlo model, Langmuir, Volume 21, Issue 24, Pages 11528-11533, 2005.
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57. Jiangyan Feng, Jiming Chen, Balaji Selvam and Diwakar Shukla*, Computational microscopy: Revealing molecular mechanisms in plants using molecular dynamics simulations, The Plant Cell, Volume 31, Issue 12, doi:10.1105/tpc.119.tt1219, 2019.