Diwakar Shukla - Publications

Affiliations: 
University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 

28 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Mohammadi E, Zhao C, Meng Y, Qu G, Zhang F, Zhao X, Mei J, Zuo JM, Shukla D, Diao Y. Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films. Nature Communications. 8: 16070. PMID 28703136 DOI: 10.1038/ncomms16070  0.44
2016 Shukla D, Peck A, Pande VS. Corrigendum: Conformational heterogeneity of the calmodulin binding interface. Nature Communications. 7: 12318. PMID 27506931 DOI: 10.1038/ncomms12318  0.96
2016 Meng Y, Shukla D, Pande VS, Roux B. Transition path theory analysis of c-Src kinase activation. Proceedings of the National Academy of Sciences of the United States of America. PMID 27482115 DOI: 10.1073/pnas.1602790113  1
2016 Schwantes CR, Shukla D, Pande VS. Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2. Biophysical Journal. 110: 1716-9. PMID 27119632 DOI: 10.1016/j.bpj.2016.03.026  0.96
2016 Shukla D, Peck A, Pande VS. Conformational heterogeneity of the calmodulin binding interface. Nature Communications. 7: 10910. PMID 27040077 DOI: 10.1038/ncomms10910  0.96
2015 Harrigan MP, Shukla D, Pande VS. Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics. Journal of Chemical Theory and Computation. 11: 1094-101. PMID 26579759 DOI: 10.1021/ct5010017  0.96
2015 Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS. Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nature Chemistry. 7: 759. PMID 26291949 DOI: 10.1038/nchem.2272  0.96
2015 Weber JK, Shukla D, Pande VS. Heat dissipation guides activation in signaling proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 26240354 DOI: 10.1073/pnas.1501804112  1
2015 Vanatta DK, Shukla D, Lawrenz M, Pande VS. A network of molecular switches controls the activation of the two-component response regulator NtrC. Nature Communications. 6: 7283. PMID 26073186 DOI: 10.1038/ncomms8283  0.96
2015 Shukla D, Lawrenz M, Pande VS. Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches. Methods in Enzymology. 557: 551-72. PMID 25950981 DOI: 10.1016/bs.mie.2014.12.007  0.96
2015 Shukla D, Hernández CX, Weber JK, Pande VS. Markov state models provide insights into dynamic modulation of protein function. Accounts of Chemical Research. 48: 414-22. PMID 25625937 DOI: 10.1021/ar5002999  1
2015 Lawrenz M, Shukla D, Pande VS. Cloud computing approaches for prediction of ligand binding poses and pathways. Scientific Reports. 5: 7918. PMID 25608737 DOI: 10.1038/srep07918  1
2014 Sultan MM, Kiss G, Shukla D, Pande VS. Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 10: 5217-5223. PMID 25516725 DOI: 10.1021/ct500353m  0.96
2014 Lapidus LJ, Acharya S, Schwantes CR, Wu L, Shukla D, King M, DeCamp SJ, Pande VS. Complex pathways in folding of protein G explored by simulation and experiment. Biophysical Journal. 107: 947-55. PMID 25140430 DOI: 10.1016/j.bpj.2014.06.037  0.96
2014 Shukla D, Meng Y, Roux B, Pande VS. Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nature Communications. 5: 3397. PMID 24584478 DOI: 10.1038/ncomms4397  1
2014 Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways Nature Chemistry. 6: 15-21. PMID 24345941 DOI: 10.1038/nchem.1821  1
2013 Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, et al. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. Journal of Chemical Theory and Computation. 9: 461-469. PMID 23316124 DOI: 10.1021/ct300857j  0.96
2013 Lane TJ, Shukla D, Beauchamp KA, Pande VS. To milliseconds and beyond: Challenges in the simulation of protein folding Current Opinion in Structural Biology. 23: 58-65. PMID 23237705 DOI: 10.1016/j.sbi.2012.11.002  1
2011 Schneider CP, Shukla D, Trout BL. Effects of solute-solute interactions on protein stability studied using various counterions and dendrimers. Plos One. 6: e27665. PMID 22125620 DOI: 10.1371/journal.pone.0027665  1
2011 Shukla D, Schneider CP, Trout BL. Complex interactions between molecular ions in solution and their effect on protein stability. Journal of the American Chemical Society. 133: 18713-8. PMID 21973239 DOI: 10.1021/ja205215t  1
2011 Shukla D, Trout BL. Understanding the synergistic effect of arginine and glutamic acid mixtures on protein solubility. The Journal of Physical Chemistry. B. 115: 11831-9. PMID 21894928 DOI: 10.1021/jp204462t  1
2011 Shukla D, Schneider CP, Trout BL. Molecular level insight into intra-solvent interaction effects on protein stability and aggregation. Advanced Drug Delivery Reviews. 63: 1074-85. PMID 21762737 DOI: 10.1016/j.addr.2011.06.014  1
2011 Schneider CP, Shukla D, Trout BL. Arginine and the Hofmeister Series: the role of ion-ion interactions in protein aggregation suppression. The Journal of Physical Chemistry. B. 115: 7447-58. PMID 21568311 DOI: 10.1021/jp111920y  1
2011 Shukla D, Zamolo L, Cavallotti C, Trout BL. Understanding the role of arginine as an eluent in affinity chromatography via molecular computations. The Journal of Physical Chemistry. B. 115: 2645-54. PMID 21355601 DOI: 10.1021/jp111156z  1
2011 Shukla D, Trout BL. Preferential interaction coefficients of proteins in aqueous arginine solutions and their molecular origins. The Journal of Physical Chemistry. B. 115: 1243-53. PMID 21186800 DOI: 10.1021/jp108586b  1
2010 Shukla D, Trout BL. Interaction of arginine with proteins and the mechanism by which it inhibits aggregation. The Journal of Physical Chemistry. B. 114: 13426-38. PMID 20925358 DOI: 10.1021/jp108399g  1
2009 Shukla D, Joshi AA, Mehra A. Modeling of formation of nanoparticles in reverse micellar systems: Ostwald ripening of silver halide particles. Langmuir : the Acs Journal of Surfaces and Colloids. 25: 3786-93. PMID 19708254 DOI: 10.1021/la803684y  1
2009 Shukla D, Shinde C, Trout BL. Molecular computations of preferential interaction coefficients of proteins. The Journal of Physical Chemistry. B. 113: 12546-54. PMID 19697945 DOI: 10.1021/jp810949t  1
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