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Automatic Feature Selection in Markov State Models Using Genetic Algorithm.

Qihua Chen#+, Jiangyan Feng+, Shriyaa Mittal and Diwakar Shukla. (#denotes undergraduate first-author, + denotes co-first author)
In review, 2018.

Molecular Basis of Glucose Transport Mechanism in Plants.

Balaji Pannerselvam, Ya-Chi Yu, Li-Qing Chen and Diwakar Shukla
In review, 2018.

Dewetting Controls Plant Hormone Perception and Initiation of Drought Resistance Signaling.

Saurabh Shukla+, Chuankai Zhao+ and Diwakar Shukla. (+ denotes co-first author)
In review, 2018.

Universality of Sodium Ion Binding Mechanism in G-Protein-Coupled Receptors

Balaji Pannerselvam, Zahra Shamsi and Diwakar Shukla
Angewandte Chemie, Vol. 47, Issue 12, Pages 3048-3053, 2018.

Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings.

Jiangyan Feng and Diwakar Shukla
The Journal of Physical Chemistry B, Volume 122, Issue 3, Pages 1017–1025, 2018.

Recruiting Machine Learning Methods for Molecular Simulations of Proteins

Shriyaa Mittal and Diwakar Shukla
Molecular Simulation, Vol. 44, Issue 11, Pages 891-904, 2018.

Using Molecular Simulation to Explore the Nanoscale Dynamics of the Plant Kinome.

Alexander S. Moffett and Diwakar Shukla
Biochemical Journal, Vol. 475, Issue 5, Pages 905-921, 2018.

Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity.

Shriyaa Mittal and Diwakar Shukla
Journal of Physical Chemistry B, Volume 121, Issue 42, Pages 9761–9770, 2017.

Allosteric control of a plant receptor kinase through S-glutathionylation.

Alexander S. Moffett, Kyle W. Bender, Steven C. Huber, and Diwakar Shukla
Biophysical Journal, Volume 113, Issue 11, Pages 2354-2363, 2017.

Free energy landscape of the complete transport cycle in a key bacterial transporter

Balaji Pannerselvam+, Shriyaa Mittal+ and Diwakar Shukla (+ denotes co-first author)
In review, 2017.

Enhanced unbiased sampling of protein dynamics using evolutionary coupling information.

Zahra Shamsi*, Alexander S. Moffett* and Diwakar Shukla. * indicates co-first author.
Scientific Reports, 7, Article number: 12700, 2017. doi:10.1038/s41598-017-12874-7

Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases.

Alexander S. Moffett, Kyle W. Bender, Steven C. Huber and Diwakar Shukla
Journal of Biological Chemistry, 292, 30, 12643–12652, 2017.

Crops in silico: A prospectus from the Plants in silico symposium and workshop

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, David Raila, Rachel G. Shekar, Stuti Shrivastava, Diwakar Shukla, Venkatraman Srinivasan, Mark Stitt, Eberhard O. Voit, Yu Wang, Xinyou Yin, Xin-Guang Zhu
Frontiers in Plant Science, Vol. 8, Article 786, 2017. doi: 10.3389/fpls.2017.00786

Dynamic-Template-Directed Multiscale Assembly for Large-Area Coating of Highly-Aligned Conjugated Polymer Thin Films

Erfan Mohammadi, Chuankai Zhao, Y. Meng, Fengjiao Zhang, Ge Qu, X. Zhao, Jianguo Mei, J. M. Zuo, Diwakar Shukla, Ying Diao.
Nature Communications, Vol. 8, Article number: 16070, 2017. doi:10.1038/ncomms16070

Application of Hidden Markov Models in Biomolecular Simulations

Book ChapterIllinois
Saurabh Shukla, Zahra Shamsi, Alexander S. Moffett, Balaji Selvam and Diwakar Shukla*
Methods in Molecular Biology, Hidden Markov Models, pp 29-41, 2017.

Conformational Heterogeneity of the Calmodulin Binding Interface.

Diwakar Shukla*, Ariana Peck* and Vijay S. Pande
Nature Communications, 7, Article number: 10910, 2016. doi:10.1038/ncomms10910

Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-computing Approaches.

Book ChapterIllinoisStanford
Diwakar Shukla*, Morgan Lawrenz and Vijay S. Pande
Methods in Enzymology, 557, 551-572, 2015.