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Import mechanism of the human serotonin transporter

Heather J. Young #, Balaji Selvam#, Matthew Chan#, Steven K. Szymanski, Diwakar Shukla*, and Erik Procko*
In review, 2019.

Transfer learning in Markov random field models.

Zahra Shamsi, Matthew Chan, Kevin S. Gill, Erik Procko and Diwakar Shukla
In review, 2019.

Ion Gel Dynamic Templates for Large Modulation of Morphology and Charge Transport Properties of Solution-Coated Conjugated Polymer Thin Films.

Erfan Mohammadi, Chuankai Zhao, Fengjiao Zhang, Ge Qu, Seok-Heon Jung, Qiujie Zhao, Christopher M. Evans, Jin-Kyun Lee, Diwakar Shukla and Ying Diao.
In review, 2019.

Molecular Basis of Glucose Transport Mechanism in Plants.

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

Divalent Cations Enhance TALE DNA-binding Specificity.

Luke Cuculis+, Chuankai Zhao+, Zhanar Abil, Huimin Zhao, Diwakar Shukla* and C. M. Schroeder*. (+ denotes co-first author)
In review, 2019.

Dodine as a Kosmo-chaotropic Agent.

Drishti Guin, Shriyaa Mittal, Brian Bozymski, Diwakar Shukla* and Martin H. W. Gruebele*
In review, 2019.

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

Saurabh Shukla+, Chuankai Zhao+ and Diwakar Shukla. (+ denotes co-first author)
Structure, Volume 27, Pages 1–11, 2019.

Selection of the Dimeric Sweet Taste Receptor for Surface Expression and Inter-subunit Interactions.

Jihye Park, Balaji Selvam, , Keisuke Sanematsu, Noriatsu Shigemura, Diwakar Shukla, and Erik Procko.
Journal of Biological Chemistry, In press, 2019.

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

Balaji Pannerselvam+, Shriyaa Mittal+ and Diwakar Shukla (+ denotes co-first author)
ACS Central Science, Volume 4, Issue 9, Pages 1146–1154, 2018.

SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes

Chuankai Zhao and Diwakar Shukla
Scientific Reports, Volume 8, Article number: 17748, 2018.

Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy Experiments

Shriyaa Mittal and Diwakar Shukla
Journal of Physical Chemistry B, Volume 122, Issue 48, Pages 10793–10805, 2018

REinforcement learning based Adaptive samPling: REAPing Rewards by Exploring Protein Conformational Landscapes

Zahra Shamsi, Kevin J. Cheng and Diwakar Shukla
Journal of Physical Chemistry B, Volume 122, Issue 35, Pages 8386–8395, 2018.

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)
Journal of Computational Science Education, Volume 9, Issue 2, Pages 14-22, 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.

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.

Recruiting Machine Learning Methods for Molecular Simulations of Proteins

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

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.