Diwakar Shukla

Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 87

Top Venues

bioRxiv : the preprint server for biology

The journal of physical chemistry. B

Communications biology

Nature communications

University of Illinois at Urbana-Champaign

Massachusetts Institute of Technology (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Illinois at Urbana-Champaign

United States

Assistant Professor :: Chemical & Biomolecular Engineering

Education History

Massachusetts Institute of Technology

United States

PHD :: Chemical Engineering

Publications

Anh T P Nguyen, Austin T Weigle, Diwakar Shukla
Functional regulation of aquaporin dynamics by lipid bilayer composition. Nature communications 15 (1) (2024)
Austin T Weigle, Diwakar Shukla
Interplay between phosphorylation and oligomerization tunes the conformational ensemble of SWEET transporters. bioRxiv : the preprint server for biology (2024)
Anh T P Nguyen, Austin T Weigle, Diwakar Shukla
Functional regulation of aquaporin dynamics by lipid bilayer composition. Nature communications 15 (1) (2024)
Balaji Selvam, Arnav Paul, Ya-Chi Yu, Li-Qing Chen, Diwakar Shukla
SWEET family transporters act as water conducting carrier proteins in plants. bioRxiv : the preprint server for biology (2024)
Jiming Chen, Tanner J Dean, Diwakar Shukla
Contribution of Signaling Partner Association to Strigolactone Receptor Selectivity. The journal of physical chemistry. B (2024)
Austin T Weigle, Diwakar Shukla
The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition. Communications biology 7 (1) (2024)
Austin T Weigle, Diwakar Shukla
Interplay between phosphorylation and oligomerization tunes the conformational ensemble of SWEET transporters. bioRxiv : the preprint server for biology (2024)
Anh T P Nguyen, Austin T Weigle, Diwakar Shukla
Functional regulation of aquaporin dynamics by lipid bilayer composition. Nature communications 15 (1) (2024)
Krishna K Narayanan, Austin T Weigle, Lingyun Xu, Xuenan Mi, Chen Zhang, Li-Qing Chen, Erik Procko, Diwakar Shukla
Deep mutational scanning reveals sequence to function constraints for SWEET family transporters. bioRxiv : the preprint server for biology (2024)
Song Yin, Xuenan Mi, Diwakar Shukla
Leveraging machine learning models for peptide-protein interaction prediction. RSC chemical biology 5 (5) (2024)
Krishna K Narayanan, Austin T Weigle, Lingyun Xu, Xuenan Mi, Chen Zhang, Li-Qing Chen, Erik Procko, Diwakar Shukla
Deep mutational scanning reveals sequence to function constraints for SWEET family transporters. bioRxiv : the preprint server for biology (2024)
Austin T Weigle, Diwakar Shukla
Interplay between phosphorylation and oligomerization tunes the conformational ensemble of SWEET transporters. bioRxiv : the preprint server for biology (2024)
Song Yin, Xuenan Mi, Diwakar Shukla
Leveraging machine learning models for peptide-protein interaction prediction. RSC chemical biology 5 (5) (2024)
Jiming Chen, Tanner J Dean, Diwakar Shukla
Contribution of Signaling Partner Association to Strigolactone Receptor Selectivity. The journal of physical chemistry. B 128 (3) (2024)
Austin T Weigle, Diwakar Shukla
The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition. Communications biology 7 (1) (2024)
Song Yin, Xuenan Mi, Diwakar Shukla
Leveraging machine learning models for peptide-protein interaction prediction. RSC chemical biology 5 (5) (2024)
Austin T Weigle, Diwakar Shukla
The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition. Communications biology 7 (1) (2024)
Song Yin, Xuenan Mi, Diwakar Shukla
Leveraging machine learning models for peptide-protein interaction prediction. RSC chemical biology 5 (5) (2024)
Susanna E Barrett, Song Yin, Peter Jordan, John K Brunson, Jessica Gordon-Nunez, Gabriella Costa Machado da Cruz, Christopher Rosario, Bethany K Okada, Kelsey Anderson, Thomas A Pires, Ruoyang Wang, Diwakar Shukla, Mark J Burk, Douglas A Mitchell
Substrate interactions guide cyclase engineering and lasso peptide diversification. Nature chemical biology (2024)
Austin T Weigle, Diwakar Shukla
The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition. Communications biology 7 (1) (2024)
Anh T P Nguyen, Austin T Weigle, Diwakar Shukla
Functional regulation of aquaporin dynamics by lipid bilayer composition. Nature communications 15 (1) (2024)
Jiming Chen, Tanner J Dean, Diwakar Shukla
Contribution of Signaling Partner Association to Strigolactone Receptor Selectivity. The journal of physical chemistry. B 128 (3) (2024)
Balaji Selvam, Arnav Paul, Ya-Chi Yu, Li-Qing Chen, Diwakar Shukla
SWEET family transporters act as water conducting carrier proteins in plants. bioRxiv : the preprint server for biology (2024)
Kihong Kim, Prateek D Bansal, Diwakar Shukla
Binding Position Dependent Modulation of Smoothened Activity by Cyclopamine. bioRxiv : the preprint server for biology (2024)
Balaji Selvam, Nicole Chiang, Diwakar Shukla
Energetics of substrate transport in proton-dependent oligopeptide transporters. bioRxiv : the preprint server for biology (2024)
Kihong Kim, Prateek D Bansal, Diwakar Shukla
Binding Position Dependent Modulation of Smoothened Activity by Cyclopamine. bioRxiv : the preprint server for biology (2024)
Anh T P Nguyen, Austin T Weigle, Diwakar Shukla
Functional regulation of aquaporin dynamics by lipid bilayer composition. Nature communications 15 (1) (2024)
Balaji Selvam, Nicole Chiang, Diwakar Shukla
Energetics of substrate transport in proton-dependent oligopeptide transporters. bioRxiv : the preprint server for biology (2024)
Matthew C Chan, Diwakar Shukla
The Effects of N-Linked Glycosylation on SLC6 Transporters. Journal of chemical information and modeling (2023)
Matthew C Chan, Kui K Chan, Erik Procko, Diwakar Shukla
Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization. The journal of physical chemistry. B 127 (9) (2023)
Matthew C Chan, Kui K Chan, Erik Procko, Diwakar Shukla
Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization. The journal of physical chemistry. B 127 (9) (2023)
Diego E Kleiman, Hassan Nadeem, Diwakar Shukla
Adaptive Sampling Methods for Molecular Dynamics in the Era of Machine Learning. The journal of physical chemistry. B (2023)
Soumajit Dutta, Diwakar Shukla
Transition-based reweighting and neural rational inference analysis of effects of new psychoactive substances on cannabinoid receptors. bioRxiv : the preprint server for biology (2023)
Matthew C Chan, Kui K Chan, Erik Procko, Diwakar Shukla
Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization. The journal of physical chemistry. B (2023)
Anaira Román Santiago, Song Yin, Johannes Elbert, Jiho Lee, Diwakar Shukla, Xiao Su
Imparting Selective Fluorophilic Interactions in Redox Copolymers for the Electrochemically Mediated Capture of Short-Chain Perfluoroalkyl Substances. Journal of the American Chemical Society (2023)
Shriyaa Mittal, Soumajit Dutta, Diwakar Shukla
Reconciling membrane protein simulations with experimental DEER spectroscopy data. Physical chemistry chemical physics : PCCP (2023)
Matthew C Chan, Kui K Chan, Erik Procko, Diwakar Shukla
Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization. The journal of physical chemistry. B 127 (9) (2023)
Matthew C Chan, Kui K Chan, Erik Procko, Diwakar Shukla
Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization. The journal of physical chemistry. B 127 (9) (2023)
Diego E Kleiman, Diwakar Shukla
Active Learning of the Conformational Ensemble of Proteins Using Maximum Entropy VAMPNets. Journal of chemical theory and computation (2023)
Xuenan Mi, Emily K Desormeaux, Tung T Le, Wilfred A van der Donk, Diwakar Shukla
Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization. Chemical science 14 (25) (2023)
Briana L Sobecks, Jiming Chen, Diwakar Shukla
Mechanistic Basis for Enhanced Strigolactone Sensitivity in KAI2 Triple Mutant. bioRxiv : the preprint server for biology (2023)
Shriyaa Mittal, Soumajit Dutta, Diwakar Shukla
Reconciling membrane protein simulations with experimental DEER spectroscopy data. Physical chemistry chemical physics : PCCP 25 (8) (2023)
Krishna K Narayanan, Moushimi Amaya, Natalie Tsang, Randy Yin, Alka Jays, Christopher C Broder, Diwakar Shukla, Erik Procko
The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins. bioRxiv : the preprint server for biology (2023)
Krishna K Narayanan, Moushimi Amaya, Natalie Tsang, Randy Yin, Alka Jays, Christopher C Broder, Diwakar Shukla, Erik Procko
The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins. bioRxiv : the preprint server for biology (2023)
Sarah E Lindley, Yiyang Lu, Diwakar Shukla
The Experimentalist's Guide to Machine Learning for Small Molecule Design. ACS applied bio materials (2023)
Shriyaa Mittal, Soumajit Dutta, Diwakar Shukla
Reconciling membrane protein simulations with experimental DEER spectroscopy data. Physical chemistry chemical physics : PCCP 25 (8) (2023)
Soumajit Dutta, Diwakar Shukla
Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptors. Communications biology 6 (1) (2023)
Matthew C Chan, Kui K Chan, Erik Procko, Diwakar Shukla
Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization. The journal of physical chemistry. B 127 (9) (2023)
Soumajit Dutta, Diwakar Shukla
Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptors. Communications biology 6 (1) (2023)
Krishna K Narayanan, Moushimi Amaya, Natalie Tsang, Randy Yin, Alka Jays, Christopher C Broder, Diwakar Shukla, Erik Procko
The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins. bioRxiv : the preprint server for biology (2023)
Xuenan Mi, Emily K Desormeaux, Tung T Le, Wilfred A van der Donk, Diwakar Shukla
Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization. Chemical science 14 (25) (2023)
Xuenan Mi, Emily K Desormeaux, Tung T Le, Wilfred A van der Donk, Diwakar Shukla
Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization. Chemical science 14 (25) (2023)
Soumajit Dutta, Diwakar Shukla
Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptors. Communications biology 6 (1) (2023)
Krishna K Narayanan, Moushimi Amaya, Natalie Tsang, Randy Yin, Alka Jays, Christopher C Broder, Diwakar Shukla, Erik Procko
The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins. bioRxiv : the preprint server for biology (2023)
Anh T P Nguyen, Austin T Weigle, Diwakar Shukla
Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition. bioRxiv : the preprint server for biology (2023)
Soumajit Dutta, Diwakar Shukla
Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptors. Communications biology 6 (1) (2023)
Briana L Sobecks, Jiming Chen, Diwakar Shukla
Mechanistic Basis for Enhanced Strigolactone Sensitivity in KAI2 Triple Mutant. bioRxiv : the preprint server for biology (2023)
Briana L Sobecks, Jiming Chen, Diwakar Shukla
Mechanistic Basis for Enhanced Strigolactone Sensitivity in KAI2 Triple Mutant. bioRxiv : the preprint server for biology (2023)
Matthew C Chan, Kui K Chan, Erik Procko, Diwakar Shukla
Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization. The journal of physical chemistry. B (2023)
Diego E Kleiman, Diwakar Shukla
Multiagent Reinforcement Learning-Based Adaptive Sampling for Conformational Dynamics of Proteins. Journal of chemical theory and computation 18 (9) (2022)
Chuankai Zhao, Diwakar Shukla
Molecular basis of the activation and dissociation of dimeric PYL2 receptor in abscisic acid signaling. Physical chemistry chemical physics : PCCP 24 (2) (2022)
Michael I Jacobs, Prateek Bansal, Diwakar Shukla, Charles M Schroeder
Understanding Supramolecular Assembly of Supercharged Proteins. ACS central science 8 (9) (2022)
Jiming Chen, Diwakar Shukla
Integration of machine learning with computational structural biology of plants. The Biochemical journal 479 (8) (2022)
Xuenan Mi, Diwakar Shukla
Predicting the Activities of Drug Excipients on Biological Targets using One-Shot Learning. The journal of physical chemistry. B 126 (7) (2022)
Soumajit Dutta, Balaji Selvam, Diwakar Shukla
Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid Receptors. ACS chemical neuroscience 13 (3) (2022)
Jiming Chen, David C Nelson, Diwakar Shukla
Activation Mechanism of Strigolactone Receptors and Its Impact on Ligand Selectivity between Host and Parasitic Plants. Journal of chemical information and modeling 62 (7) (2022)
Austin T Weigle, Jiangyan Feng, Diwakar Shukla
Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Physical chemistry chemical physics : PCCP 24 (43) (2022)
Matthew C Chan, Erik Procko, Diwakar Shukla
Structural Rearrangement of the Serotonin Transporter Intracellular Gate Induced by Thr276 Phosphorylation. ACS chemical neuroscience 13 (7) (2022)
Jesse Horne, Diwakar Shukla
Recent Advances in Machine Learning Variant Effect Prediction Tools for Protein Engineering. Industrial & engineering chemistry research 61 (19) (2022)
Briana L Sobecks, Jiming Chen, Diwakar Shukla
Dual Role of Strigolactone Receptor Signaling Partner in Inhibiting Substrate Hydrolysis. The journal of physical chemistry. B 126 (11) (2022)
Lars H Kruse, Austin T Weigle, Mohammad Irfan, Jesús Martínez-Gómez, Jason D Chobirko, Jason E Schaffer, Alexandra A Bennett, Chelsea D Specht, Joseph M Jez, Diwakar Shukla, Gaurav D Moghe
Orthology-based analysis helps map evolutionary diversification and predict substrate class use of BAHD acyltransferases. The Plant journal : for cell and molecular biology 111 (5) (2022)
Austin T Weigle, Matthew Carr, Diwakar Shukla
Impact of Increased Membrane Realism on Conformational Sampling of Proteins. Journal of chemical theory and computation 17 (8) (2021)
Matthew C Chan, Kui K Chan, Erik Procko, Diwakar Shukla
Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. bioRxiv : the preprint server for biology (2021)
Faisal Aldukhi, Aniket Deb, Chuankai Zhao, Alexander S Moffett, Diwakar Shukla
Molecular Mechanism of Brassinosteroid Perception by the Plant Growth Receptor BRI1. The journal of physical chemistry. B 124 (2) (2020)
Jiangyan Feng, Diwakar Shukla
FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution. The journal of physical chemistry. B 124 (18) (2020)
Zahra Shamsi, Matthew C Chan, Diwakar Shukla
TLmutation: Predicting the Effects of Mutations Using Transfer Learning. The journal of physical chemistry. B 124 (19) (2020)
Erfan Mohammadi, Chuankai Zhao, Fengjiao Zhang, Ge Qu, Seok-Heon Jung, Qiujie Zhao, Christopher M Evans, Jin-Kyun Lee, Diwakar Shukla, Ying Diao
Ion Gel Dynamic Templates for Large Modulation of Morphology and Charge Transport Properties of Solution-Coated Conjugated Polymer Thin Films. ACS applied materials & interfaces 11 (25) (2019)
Kevin J Cheng, Balaji Selvam, Li-Qing Chen, Diwakar Shukla
Distinct Substrate Transport Mechanism Identified in Homologous Sugar Transporters. The journal of physical chemistry. B 123 (40) (2019)
Drishti Guin, Shriyaa Mittal, Brian Bozymski, Diwakar Shukla, Martin Gruebele
Dodine as a Kosmo-Chaotropic Agent. The journal of physical chemistry letters 10 (10) (2019)
Shriyaa Mittal, Diwakar Shukla
Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy Experiments. The journal of physical chemistry. B 122 (48) (2018)
Zahra Shamsi, Kevin J Cheng, Diwakar Shukla
Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes. The journal of physical chemistry. B 122 (35) (2018)
Chuankai Zhao, Diwakar Shukla
SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes. Scientific reports 8 (1) (2018)
Balaji Selvam, Zahra Shamsi, Diwakar Shukla
Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors. Angewandte Chemie (International ed. in English) 57 (12) (2018)
Jiangyan Feng, Diwakar Shukla
Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings. The journal of physical chemistry. B 122 (3) (2018)
Zahra Shamsi, Alexander S Moffett, Diwakar Shukla
Enhanced unbiased sampling of protein dynamics using evolutionary coupling information. Scientific reports 7 (1) (2017)
Shriyaa Mittal, Diwakar Shukla
Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity. The journal of physical chemistry. B 121 (42) (2017)
Zahra Shamsi, Alexander S Moffett, Diwakar Shukla
Publisher Correction: Enhanced unbiased sampling of protein dynamics using evolutionary coupling information. Scientific reports 7 (1) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Diwakar Shukla