If you made any changes in Pure these will be visible here soon.

Research Output

  • 53 Article
  • 3 Chapter
  • 3 Review article
  • 2 Conference contribution
2020

Divalent cations promote TALE DNA-binding specificity

Cuculis, L., Zhao, C., Abil, Z., Zhao, H., Shukla, D. & Schroeder, C. M., Feb 20 2020, In : Nucleic acids research. 48, 3, p. 1406-1422 17 p.

Research output: Contribution to journalArticle

Open Access

FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution

Feng, J. & Shukla, D., May 7 2020, In : Journal of Physical Chemistry B. 124, 18, p. 3605-3615 11 p.

Research output: Contribution to journalArticle

Molecular Mechanism of Brassinosteroid Perception by the Plant Growth Receptor BRI1

Aldukhi, F., Deb, A., Zhao, C., Moffett, A. S. & Shukla, D., Jan 16 2020, In : Journal of Physical Chemistry B. 124, 2, p. 355-365 11 p.

Research output: Contribution to journalArticle

Structural Consequences of Multisite Phosphorylation in the BAK1 Kinase Domain

Moffett, A. S. & Shukla, D., Feb 4 2020, In : Biophysical journal. 118, 3, p. 698-707 10 p.

Research output: Contribution to journalArticle

TLmutation: Predicting the Effects of Mutations Using Transfer Learning

Shamsi, Z., Chan, M. & Shukla, D., May 14 2020, In : Journal of Physical Chemistry B. 124, 19, p. 3845-3854 10 p.

Research output: Contribution to journalArticle

2019

Dewetting Controls Plant Hormone Perception and Initiation of Drought Resistance Signaling

Shukla, S., Zhao, C. & Shukla, D., Apr 2 2019, In : Structure. 27, 4, p. 692-702.e3

Research output: Contribution to journalArticle

Distinct Substrate Transport Mechanism Identified in Homologous Sugar Transporters

Cheng, K. J., Selvam, B., Chen, L. Q. & Shukla, D., Oct 10 2019, In : Journal of Physical Chemistry B. 123, 40, p. 8411-8418 8 p.

Research output: Contribution to journalArticle

Dodine as a Kosmo-Chaotropic Agent

Guin, D., Mittal, S., Bozymski, B., Shukla, D. & Gruebele, M., May 16 2019, In : Journal of Physical Chemistry Letters. 10, 10, p. 2600-2605 6 p.

Research output: Contribution to journalArticle

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

Mohammadi, E., Zhao, C., Zhang, F., Qu, G., Jung, S. H., Zhao, Q., Evans, C., Lee, J. K., Shukla, D. & Diao, Y., Jan 1 2019, In : ACS Applied Materials and Interfaces.

Research output: Contribution to journalArticle

Molecular Basis of the Glucose Transport Mechanism in Plants

Selvam, B., Yu, Y. C., Chen, L. Q. & Shukla, D., Jun 26 2019, In : ACS Central Science. 5, 6, p. 1085-1096 12 p.

Research output: Contribution to journalArticle

Open Access

Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits

Park, J., Selvam, B., Sanematsu, K., Shigemura, N., Shukla, D. & Procko, E., Mar 29 2019, In : Journal of Biological Chemistry. 294, 13, p. 4759-4774 16 p.

Research output: Contribution to journalArticle

2018

Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings

Feng, J. & Shukla, D., Jan 25 2018, In : Journal of Physical Chemistry B. 122, 3, p. 1017-1025 9 p.

Research output: Contribution to journalArticle

Free Energy Landscape of the Complete Transport Cycle in a Key Bacterial Transporter

Selvam, B., Mittal, S. & Shukla, D., Sep 26 2018, In : ACS Central Science. 4, 9, p. 1146-1154 9 p.

Research output: Contribution to journalArticle

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

Mittal, S. & Shukla, D., Dec 6 2018, In : Journal of Physical Chemistry B. 122, 48, p. 10793-10805 13 p.

Research output: Contribution to journalArticle

Recruiting machine learning methods for molecular simulations of proteins

Mittal, S. & Shukla, D., Jul 24 2018, In : Molecular Simulation. 44, 11, p. 891-904 14 p.

Research output: Contribution to journalArticle

Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes

Shamsi, Z., Cheng, K. J. & Shukla, D., Sep 6 2018, In : Journal of Physical Chemistry B. 122, 35, p. 8386-8395 10 p.

Research output: Contribution to journalArticle

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

Zhao, C. & Shukla, D., Dec 1 2018, In : Scientific reports. 8, 1, 17748.

Research output: Contribution to journalArticle

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

Selvam, B., Shamsi, Z. & Shukla, D., Mar 12 2018, In : Angewandte Chemie - International Edition. 57, 12, p. 3048-3053 6 p.

Research output: Contribution to journalArticle

Using molecular simulation to explore the nanoscale dynamics of the plant kinome

Moffett, A. S. & Shukla, D., Mar 15 2018, In : Biochemical Journal. 475, 5, p. 905-921 17 p.

Research output: Contribution to journalArticle

2017

Allosteric Control of a Plant Receptor Kinase through S-Glutathionylation

Moffett, A. S., Bender, K. W., Huber, S. C. & Shukla, D., Dec 5 2017, In : Biophysical journal. 113, 11, p. 2354-2363 10 p.

Research output: Contribution to journalArticle

Application of Hidden Markov models in biomolecular simulations

Shukla, S., Shamsi, Z., Moffett, A. S., Selvam, B. & Shukla, D., Jan 1 2017, Methods in Molecular Biology. Humana Press Inc., Vol. 1552. p. 29-41 13 p. (Methods in Molecular Biology; vol. 1552).

Research output: Chapter in Book/Report/Conference proceedingChapter

Crops in silico: Generating virtual crops using an integrative and multi-scale modeling platform

Marshall-Colon, A., Long, S. P., Allen, D. K., Allen, G. D., Beard, D. A., Benes, B., Von Caemmerer, S., Christensen, A. J., Cox, D. J., Hart, J. C., Hirst, P. M., Kannan, K., Katz, D. S., Lynch, J. P., Millar, A. J., Panneerselvam, B., Price, N. D., Prusinkiewicz, P., Raila, D., Shekar, R. G. & 9 others, Shrivastava, S., Shukla, D., Srinivasan, V., Stitt, M., Turk, M. J., Voit, E. O., Wang, Y., Yin, X. & Zhu, X. G., May 15 2017, In : Frontiers in Plant Science. 8, 786.

Research output: Contribution to journalArticle

Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films

Mohammadi, E., Zhao, C., Meng, Y., Qu, G., Zhang, F., Zhao, X., Mei, J., Zuo, J. M., Shukla, D. & Diao, Y., Jul 13 2017, In : Nature communications. 8, 16070.

Research output: Contribution to journalArticle

Enhanced unbiased sampling of protein dynamics using evolutionary coupling information

Shamsi, Z., Moffett, A. S. & Shukla, D., Dec 1 2017, In : Scientific reports. 7, 1, 12700.

Research output: Contribution to journalArticle

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

Moffett, A. S., Bender, K. W., Huber, S. C. & Shukla, D., Jul 21 2017, In : Journal of Biological Chemistry. 292, 30, p. 12643-12652 10 p.

Research output: Contribution to journalArticle

Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity

Mittal, S. & Shukla, D., Oct 26 2017, In : Journal of Physical Chemistry B. 121, 42, p. 9761-9770 10 p.

Research output: Contribution to journalArticle

2016

Conformational heterogeneity of the calmodulin binding interface

Shukla, D., Peck, A. & Pande, V. S., Apr 4 2016, In : Nature communications. 7, 10910.

Research output: Contribution to journalArticle

Markov state models and tICA reveal a nonnative folding nucleus in simulations of NuG2

Schwantes, C. R., Shukla, D. & Pande, V. S., Apr 26 2016, In : Biophysical journal. 110, 8, p. 1716-1719 4 p.

Research output: Contribution to journalArticle

Transition path theory analysis of c-Src kinase activation

Meng, Y., Shukla, D., Pande, V. S. & Roux, B., Aug 16 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 33, p. 9193-9198 6 p.

Research output: Contribution to journalArticle

2015

A network of molecular switches controls the activation of the two-component response regulator NtrC

Vanatta, D. K., Shukla, D., Lawrenz, M. & Pande, V. S., Jun 15 2015, In : Nature communications. 6, 7283.

Research output: Contribution to journalArticle

Cloud computing approaches for prediction of ligand binding poses and pathways

Lawrenz, M., Shukla, D. & Pande, V. S., Jan 22 2015, In : Scientific reports. 5, 7918.

Research output: Contribution to journalArticle

Conserve water: A method for the analysis of solvent in molecular dynamics

Harrigan, M. P., Shukla, D. & Pande, V. S., Mar 10 2015, In : Journal of Chemical Theory and Computation. 11, 3, p. 1094-1101 8 p.

Research output: Contribution to journalArticle

Elucidating ligand-modulated conformational landscape of GPCRs using cloud-computing approaches

Shukla, D., Lawrenz, M. & Pande, V. S., Jan 1 2015, Methods in Enzymology. Academic Press Inc., p. 551-572 22 p. (Methods in Enzymology; vol. 557).

Research output: Chapter in Book/Report/Conference proceedingChapter

Heat dissipation guides activation in signaling proteins

Weber, J. K., Shukla, D. & Pande, V. S., Aug 18 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 33, p. 10377-10382 6 p.

Research output: Contribution to journalArticle

Markov state models provide insights into dynamic modulation of protein function

Shukla, D., Hernández, C. X., Weber, J. K. & Pande, V. S., Feb 17 2015, In : Accounts of chemical research. 48, 2, p. 414-422 9 p.

Research output: Contribution to journalReview article

2014

Activation pathway of Src kinase reveals intermediate states as targets for drug design

Shukla, D., Meng, Y., Roux, B. & Pande, V. S., Mar 3 2014, In : Nature communications. 5, 3397.

Research output: Contribution to journalArticle

Automatic selection of order parameters in the analysis of large scale molecular dynamics simulations

Sultan, M. M., Kiss, G., Shukla, D. & Pande, V. S., Dec 9 2014, In : Journal of Chemical Theory and Computation. 10, 12, p. 5217-5223 7 p.

Research output: Contribution to journalArticle

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

Kohlhoff, K. J., Shukla, D., Lawrenz, M., Bowman, G. R., Konerding, D. E., Belov, D., Altman, R. B. & Pande, V. S., Jan 2014, In : Nature Chemistry. 6, 1, p. 15-21 7 p.

Research output: Contribution to journalArticle

Complex pathways in folding of protein G explored by simulation and experiment

Lapidus, L. J., Acharya, S., Schwantes, C. R., Wu, L., Shukla, D., King, M., Decamp, S. J. & Pande, V. S., Aug 19 2014, In : Biophysical journal. 107, 4, p. 947-955 9 p.

Research output: Contribution to journalArticle

2013

OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation

Eastman, P., Friedrichs, M. S., Chodera, J. D., Radmer, R. J., Bruns, C. M., Ku, J. P., Beauchamp, K. A., Lane, T. J., Wang, L. P., Shukla, D., Tye, T., Houston, M., Stich, T., Klein, C., Shirts, M. R. & Pande, V. S., Jan 8 2013, In : Journal of Chemical Theory and Computation. 9, 1, p. 461-469 9 p.

Research output: Contribution to journalArticle

To milliseconds and beyond: Challenges in the simulation of protein folding

Lane, T. J., Shukla, D., Beauchamp, K. A. & Pande, V. S., Feb 1 2013, In : Current Opinion in Structural Biology. 23, 1, p. 58-65 8 p.

Research output: Contribution to journalReview article

Understanding the role of arginine and citrate as eluents in affinity chromatography

Shukla, D. & Trout, B. L., Mar 8 2013, Developments in Biotechnology and Bioprocessing. American Chemical Society, p. 67-86 20 p. (ACS Symposium Series; vol. 1125).

Research output: Chapter in Book/Report/Conference proceedingChapter

2011

Arginine and the hofmeister series: The role of ion-ion interactions in protein aggregation suppression

Schneider, C. P., Shukla, D. & Trout, B. L., Jun 9 2011, In : Journal of Physical Chemistry B. 115, 22, p. 7447-7458 12 p.

Research output: Contribution to journalArticle

Complex interactions between molecular ions in solution and their effect on protein stability

Shukla, D., Schneider, C. P. & Trout, B. L., Nov 23 2011, In : Journal of the American Chemical Society. 133, 46, p. 18713-18718 6 p.

Research output: Contribution to journalArticle

Effects of PAMAM dendrimer salt solutions on protein stability

Shukla, D., Schneider, C. P. & Trout, B. L., Jul 21 2011, In : Journal of Physical Chemistry Letters. 2, 14, p. 1782-1788 7 p.

Research output: Contribution to journalArticle

Effects of Solute-Solute Interactions on Protein Stability Studied Using Various Counterions and Dendrimers

Schneider, C. P., Shukla, D. & Trout, B. L., Dec 1 2011, In : PloS one. 6, 11, e27665.

Research output: Contribution to journalArticle

Molecular level insight into intra-solvent interaction effects on protein stability and aggregation

Shukla, D., Schneider, C. P. & Trout, B. L., Oct 1 2011, In : Advanced Drug Delivery Reviews. 63, 13, p. 1074-1085 12 p.

Research output: Contribution to journalReview article

Preferential interaction coefficients of proteins in aqueous arginine solutions and their molecular origins

Shukla, D. & Trout, B. L., Feb 10 2011, In : Journal of Physical Chemistry B. 115, 5, p. 1243-1253 11 p.

Research output: Contribution to journalArticle

Understanding the role of arginine as an eluent in affinity chromatography via molecular computations

Shukla, D., Zamolo, L., Cavallotti, C. & Trout, B. L., Mar 24 2011, In : Journal of Physical Chemistry B. 115, 11, p. 2645-2654 10 p.

Research output: Contribution to journalArticle