| Year |
Citation |
Score |
| 2024 |
Narayanan KK, Weigle AT, Xu L, Mi X, Zhang C, Chen LQ, Procko E, Shukla D. Deep mutational scanning reveals sequence to function constraints for SWEET family transporters. Biorxiv : the Preprint Server For Biology. PMID 39005363 DOI: 10.1101/2024.06.28.601307 |
0.764 |
|
| 2024 |
Weigle AT, Shukla D. Interplay between phosphorylation and oligomerization tunes the conformational ensemble of SWEET transporters. Biorxiv : the Preprint Server For Biology. PMID 38915650 DOI: 10.1101/2024.06.12.598708 |
0.775 |
|
| 2024 |
Weigle AT, Shukla D. The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition. Communications Biology. 7: 764. PMID 38914639 DOI: 10.1038/s42003-024-06291-6 |
0.76 |
|
| 2024 |
Nguyen ATP, Weigle AT, Shukla D. Functional regulation of aquaporin dynamics by lipid bilayer composition. Nature Communications. 15: 1848. PMID 38418487 DOI: 10.1038/s41467-024-46027-y |
0.782 |
|
| 2023 |
Nguyen ATP, Weigle AT, Shukla D. Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition. Biorxiv : the Preprint Server For Biology. PMID 37502896 DOI: 10.1101/2023.07.20.549977 |
0.782 |
|
| 2023 |
Mittal S, Dutta S, Shukla D. Reconciling membrane protein simulations with experimental DEER spectroscopy data. Physical Chemistry Chemical Physics : Pccp. 25: 6253-6262. PMID 36757376 DOI: 10.1039/d2cp02890e |
0.348 |
|
| 2022 |
Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Physical Chemistry Chemical Physics : Pccp. 24: 26371-26397. PMID 36285789 DOI: 10.1039/d2cp02883b |
0.797 |
|
| 2022 |
Kruse LH, Weigle AT, Irfan M, Martínez-Gómez J, Chobirko JD, Schaffer JE, Bennett AA, Specht CD, Jez JM, Shukla D, Moghe GD. Orthology-based analysis helps map evolutionary diversification and predict substrate class use of BAHD acyltransferases. The Plant Journal : For Cell and Molecular Biology. PMID 35816116 DOI: 10.1111/tpj.15902 |
0.751 |
|
| 2022 |
Dutta S, Selvam B, Das A, Shukla D. Mechanistic origin of partial agonism of tetrahydrocannabinol for cannabinoid receptors. The Journal of Biological Chemistry. 298: 101764. PMID 35227761 DOI: 10.1016/j.jbc.2022.101764 |
0.575 |
|
| 2021 |
Chan MC, Shukla D. Markov state modeling of membrane transport proteins. Journal of Structural Biology. 107800. PMID 34600140 DOI: 10.1016/j.jsb.2021.107800 |
0.351 |
|
| 2021 |
Weigle AT, Carr M, Shukla D. Impact of Increased Membrane Realism on Conformational Sampling of Proteins. Journal of Chemical Theory and Computation. PMID 34339605 DOI: 10.1021/acs.jctc.1c00276 |
0.773 |
|
| 2020 |
Feng J, Shukla D. FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution. The Journal of Physical Chemistry. B. PMID 32283936 DOI: 10.1021/Acs.Jpcb.9B11869 |
0.355 |
|
| 2020 |
Moffett AS, Shukla D. Structural Consequences of Multisite Phosphorylation in the BAK1 Kinase Domain. Biophysical Journal. PMID 31962105 DOI: 10.1016/J.Bpj.2019.12.026 |
0.337 |
|
| 2020 |
Mittal S, Shukla D. Reconciling Membrane Protein Simulations with Experimental Spectroscopic Data Biophysical Journal. 118: 231a. DOI: 10.1016/J.Bpj.2019.11.1367 |
0.389 |
|
| 2019 |
Aldukhi F, Deb A, Zhao C, Moffett AS, Shukla D. Molecular Mechanism of Brassinosteroids Perception by the Plant Growth Receptor BRI1. The Journal of Physical Chemistry. B. PMID 31873025 DOI: 10.1021/Acs.Jpcb.9B09377 |
0.36 |
|
| 2019 |
Cuculis L, Zhao C, Abil Z, Zhao H, Shukla D, Schroeder CM. Divalent cations promote TALE DNA-binding specificity. Nucleic Acids Research. PMID 31863586 DOI: 10.1093/Nar/Gkz1174 |
0.327 |
|
| 2019 |
Cheng KJ, Selvam B, Chen LQ, Shukla D. Distinct Substrate Transport Mechanism Identified in Homologous Sugar Transporters. The Journal of Physical Chemistry. B. PMID 31498631 DOI: 10.1021/Acs.Jpcb.9B08257 |
0.392 |
|
| 2019 |
Selvam B, Yu YC, Chen LQ, Shukla D. Molecular Basis of the Glucose Transport Mechanism in Plants. Acs Central Science. 5: 1085-1096. PMID 31263768 DOI: 10.1021/Acscentsci.9B00252 |
0.367 |
|
| 2019 |
Guin D, Mittal S, Bozymski B, Shukla D, Gruebele M. Dodine as a Kosmo-Chaotropic Agent. The Journal of Physical Chemistry Letters. PMID 31026167 DOI: 10.1021/Acs.Jpclett.9B00379 |
0.357 |
|
| 2019 |
Mittal S, Shukla D. Simulation Guided Design of Spectroscopy Experiments via Maximizing Kinetic Information Gain Biophysical Journal. 116: 183a-184a. DOI: 10.1016/J.Bpj.2018.11.1020 |
0.303 |
|
| 2018 |
Shukla S, Zhao C, Shukla D. Dewetting Controls Plant Hormone Perception and Initiation of Drought Resistance Signaling. Structure (London, England : 1993). PMID 30686665 DOI: 10.1016/J.Str.2018.12.005 |
0.312 |
|
| 2018 |
Zhao C, Shukla D. SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes. Scientific Reports. 8: 17748. PMID 30531946 DOI: 10.1038/S41598-018-36090-Z |
0.409 |
|
| 2018 |
Mittal S, Shukla D. Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy Experiments. The Journal of Physical Chemistry. B. PMID 30351125 DOI: 10.1021/Acs.Jpcb.8B07076 |
0.375 |
|
| 2018 |
Selvam B, Mittal S, Shukla D. Free Energy Landscape of the Complete Transport Cycle in a Key Bacterial Transporter. Acs Central Science. 4: 1146-1154. PMID 30276247 DOI: 10.1021/Acscentsci.8B00330 |
0.413 |
|
| 2018 |
Shamsi Z, Cheng KJ, Shukla D. REinforcement learning based Adaptive samPling: REAPing Rewards by Exploring Protein Conformational Landscapes. The Journal of Physical Chemistry. B. PMID 30126271 DOI: 10.1021/Acs.Jpcb.8B06521 |
0.319 |
|
| 2018 |
Moffett AS, Shukla D. Using molecular simulation to explore the nanoscale dynamics of the plant kinome. The Biochemical Journal. 475: 905-921. PMID 29523701 DOI: 10.1042/Bcj20170299 |
0.453 |
|
| 2018 |
Selvam B, Shamsi Z, Shukla D. Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors. Angewandte Chemie (International Ed. in English). 57: 3048-3053. PMID 29405531 DOI: 10.1002/Anie.201708889 |
0.322 |
|
| 2018 |
Feng J, Shukla D. Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings. The Journal of Physical Chemistry. B. 122: 1017-1025. PMID 29293335 DOI: 10.1021/Acs.Jpcb.7B07529 |
0.42 |
|
| 2018 |
Mittal S, Shukla D. Recruiting machine learning methods for molecular simulations of proteins Molecular Simulation. 44: 891-904. DOI: 10.1080/08927022.2018.1448976 |
0.441 |
|
| 2018 |
Moffett AS, Bender KW, Huber SC, Shukla D. Investigating the Conformational Dynamics of Plant Protein Kinases Biophysical Journal. 114: 582a-583a. DOI: 10.1016/J.Bpj.2017.11.3188 |
0.354 |
|
| 2017 |
Moffett AS, Bender KW, Huber SC, Shukla D. Allosteric Control of a Plant Receptor Kinase through S-Glutathionylation. Biophysical Journal. 113: 2354-2363. PMID 29211989 DOI: 10.1016/J.Bpj.2017.08.059 |
0.369 |
|
| 2017 |
Shamsi Z, Moffett AS, Shukla D. Enhanced unbiased sampling of protein dynamics using evolutionary coupling information. Scientific Reports. 7: 12700. PMID 28983093 DOI: 10.1038/S41598-017-12874-7 |
0.401 |
|
| 2017 |
Mittal S, Shukla D. Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity. The Journal of Physical Chemistry. B. PMID 28726404 DOI: 10.1021/Acs.Jpcb.7B04785 |
0.379 |
|
| 2017 |
Moffett AS, Bender KW, Huber SC, Shukla D. Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases. The Journal of Biological Chemistry. PMID 28559283 DOI: 10.1074/Jbc.M117.792762 |
0.398 |
|
| 2017 |
Marshall-Colon A, Long SP, Allen DK, Allen G, Beard DA, Benes B, von Caemmerer S, Christensen AJ, Cox DJ, Hart JC, Hirst PM, Kannan K, Katz DS, Lynch JP, Millar AJ, ... ... Shukla D, et al. Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform. Frontiers in Plant Science. 8: 786. PMID 28555150 DOI: 10.3389/Fpls.2017.00786 |
0.333 |
|
| 2017 |
Shukla S, Shamsi Z, Moffett AS, Selvam B, Shukla D. Application of Hidden Markov Models in Biomolecular Simulations. Methods in Molecular Biology (Clifton, N.J.). 1552: 29-41. PMID 28224489 DOI: 10.1007/978-1-4939-6753-7_3 |
0.406 |
|
| 2017 |
Shukla S, Meigooni M, Zhao C, Shukla D. Machine Learning Guided Ligand-Protein Simulation Approach Elucidates the Binding Mechanism of Abscisic Acid Biophysical Journal. 112: 349a. DOI: 10.1016/J.Bpj.2016.11.1892 |
0.37 |
|
| 2017 |
Selvam B, Shukla D. Understanding the Conformational Diversity of Proton-Coupled Oligopeptide Transporter (POT) Family Biophysical Journal. 112: 16a-17a. DOI: 10.1016/J.Bpj.2016.11.124 |
0.413 |
|
| 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 |
0.541 |
|
| 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 |
0.523 |
|
| 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 |
0.544 |
|
| 2016 |
Shukla D, Peck A, Pande VS. Conformational heterogeneity of the calmodulin binding interface. Nature Communications. 7: 10910. PMID 27040077 DOI: 10.1038/Ncomms10910 |
0.55 |
|
| 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 |
0.566 |
|
| 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 |
0.768 |
|
| 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 |
0.591 |
|
| 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 |
0.605 |
|
| 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 |
0.606 |
|
| 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 |
0.733 |
|
| 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 |
0.569 |
|
| 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. DOI: 10.1038/ncomms8283 |
0.391 |
|
| 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: 1094-1101. DOI: 10.1021/ct5010017 |
0.433 |
|
| 2015 |
Shukla D, Lawrenz M, Pande VS. Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches Methods in Enzymology. DOI: 10.1016/bs.mie.2014.12.007 |
0.452 |
|
| 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 |
0.578 |
|
| 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 |
0.576 |
|
| 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 |
0.56 |
|
| 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 |
0.795 |
|
| 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. DOI: 10.1021/ct500353m |
0.489 |
|
| 2014 |
Parton DL, Shukla D, Zhao Y, Pande VS, Chodera JD. Toward a Global View of the Conformational Landscape of the Human Kinome Biophysical Journal. 106: 655a-656a. DOI: 10.1016/J.Bpj.2013.11.3628 |
0.701 |
|
| 2014 |
Shukla D, Roux B, Pande VS. Activation Pathways of Kinases Reveal Intermediate States as Novel Targets for Drug Design Biophysical Journal. 106: 308a. DOI: 10.1016/J.Bpj.2013.11.1784 |
0.565 |
|
| 2014 |
Lawrenz M, Kohlhoff K, Shukla D, Bowman G, Altman R, Pande V. Investigating Ligand-Modulation of GPCR Activation Pathways Biophysical Journal. 106: 14a. DOI: 10.1016/J.Bpj.2013.11.130 |
0.802 |
|
| 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 |
0.772 |
|
| 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 |
0.6 |
|
| 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. DOI: 10.1021/ct300857j |
0.78 |
|
| 2013 |
Shukla D, Trout BL. Understanding the role of arginine and citrate as eluents in affinity chromatography Acs Symposium Series. 1125: 67-86. DOI: 10.1021/bk-2013-1125.ch005 |
0.464 |
|
| 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 |
0.568 |
|
| 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 |
0.566 |
|
| 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 |
0.58 |
|
| 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 |
0.583 |
|
| 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 |
0.575 |
|
| 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 |
0.544 |
|
| 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 |
0.568 |
|
| 2011 |
Shukla D, Schneider CP, Trout BL. Effects of PAMAM dendrimer salt solutions on protein stability Journal of Physical Chemistry Letters. 2: 1782-1788. DOI: 10.1021/Jz200758M |
0.565 |
|
| 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 |
0.593 |
|
| 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 |
0.612 |
|
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