Diwakar Shukla

Also affiliated with University of Illinois System, Quantitative BioSciences

Biochemistry, Genetics and Molecular BiologyComputer ScienceAgricultural and Biological Sciences

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 38 papers. Top paper: “Degradation of complex arabinoxylans by human colonic Bacteroidetes”.

Degradation of complex arabinoxylans by human colonic Bacteroidetes

Nature Communications(2021)10.1038/s41467-020-20737-5

N/A

0.779DataRank · unranked

179 citations

Ahmed M. Abdel-Hamid, Soumajit Dutta, Corina N. D’Alessandro‐Gabazza, Daniel Wefers, Jacob A. Farris +9 more

Leveraging machine learning models for peptide–protein interaction prediction

RSC Chemical Biology(2024)10.1039/d3cb00208j

N/A

0.590DataRank · unranked

50 citations

Xuenan Mi, Diwakar Shukla, Yin Song

Role of internal loop dynamics in antibiotic permeability of outer membrane porins

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2117009119

N/A

0.568DataRank · unranked

43 citations

Nandan Haloi, Rebecca J. Ulrich, Mary Elizabeth Metcalf, Po‐Chao Wen, William W. Metcalf +4 more

Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization

Chemical Science(2023)10.1039/d2sc06546k

N/A

0.521DataRank · unranked

16 citations

Emily K. Desormeaux, Tung Le, Wilfred A. van der Donk, Diwakar Shukla, Xuenan Mi

Substrate interactions guide cyclase engineering and lasso peptide diversification

Nature Chemical Biology(2024)10.1038/s41589-024-01727-w

N/A

0.510DataRank · unranked

29 citations

Yin Song, Peter Jordan, John K. Brunson, Jessica Gordon-Nunez, Gabriella Costa Machado da Cruz +9 more

Activation mechanism of the human Smoothened receptor

Biophysical Journal(2023)10.1016/j.bpj.2023.03.007

N/A

0.505DataRank · unranked

28 citations

Soumajit Dutta, Diwakar Shukla, Prateek D. Bansal

The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition

Communications Biology(2024)10.1038/s42003-024-06291-6

N/A

0.464DataRank · unranked

21 citations

Diwakar Shukla, Austin T. Weigle

Cyclopamine modulates smoothened receptor activity in a binding position dependent manner

Communications Biology(2024)10.1038/s42003-024-06906-y

N/A

0.425DataRank · unranked

13 citations

Prateek D. Bansal, Diwakar Shukla, Kihong Kim

The Experimentalist’s Guide to Machine Learning for Small Molecule Design

ACS Applied Bio Materials(2023)10.1021/acsabm.3c00054

N/A

0.360DataRank · unranked

10 citations

Yiyang Lu, Diwakar Shukla, Sarah E. Lindley

Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization

The Journal of Physical Chemistry B(2023)10.1021/acs.jpcb.3c00469

N/A

0.345DataRank · unranked

9 citations

Kui K. Chan, Erik Procko, Diwakar Shukla, Matthew C. Chan

Mapping Strigolactone Hydrolysis in DWARF14 via QM/MM String Method

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.22.489200

N/A

0.312DataRank · unranked

7 citations

Jiming Chen, Diwakar Shukla, Tanner J. Dean

Optimizing adaptive sampling via Policy Ranking

arXiv (Cornell University)(2024)10.48550/arxiv.2410.15259

N/A

0.165DataRank · unranked

2 citations

Diwakar Shukla, Hassan Nadeem

Thirty years of molecular dynamics simulations on posttranslational modifications of proteins

Physical Chemistry Chemical Physics(2022)10.1039/d2cp02883b

N/A

0.104DataRank · unranked

1 citations

Jiangyan Feng, Diwakar Shukla, Austin T. Weigle

Effect of Histidine Covalent Modification on Strigolactone Receptor Activation and Selectivity

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.13.499796

N/A

0.104DataRank · unranked

1 citations

Diwakar Shukla, Jiming Chen

Energetics of substrate transport in proton-dependent oligopeptide transporters

Communications Chemistry(2024)10.1038/s42004-024-01398-7

N/A

0.104DataRank · unranked

1 citations

Nicole Chiang, Diwakar Shukla, Balaji Selvam

Structure-function analysis of plant G-protein regulatory mechanisms identifies key Gα-RGS protein interactions

Journal of Biological Chemistry(2024)10.1016/j.jbc.2024.107252

N/A

0DataRank · unranked

5 citations

Soon Goo Lee, Swarup Roy Choudhury, Rabindranath Paul, Balaji Selvam, Diwakar Shukla +3 more

Binding Position Dependent Modulation of Smoothened Activity by Cyclopamine

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.08.579369

N/A

0DataRank · unranked

1 citations

Prateek D. Bansal, Diwakar Shukla, Kihong Kim

Interplay between phosphorylation and oligomerization tunes the conformational ensemble of SWEET transporters

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.12.598708

N/A

0DataRank · unranked

1 citations

Diwakar Shukla, Austin T. Weigle

LassoESM a tailored language model for enhanced lasso peptide property prediction

Nature Communications(2025)10.1038/s41467-025-63412-3

N/A

0DataRank · unranked

4 citations

Susanna E. Barrett, Douglas A. Mitchell, Diwakar Shukla, Xuenan Mi

ESMDynamic: Fast and Accurate Prediction of Protein Dynamic Contact Maps from Single Sequences

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.20.671365

N/A

0DataRank · unranked

4 citations

Jiangyan Feng, Zhengyuan Xue, Diwakar Shukla, Diego E. Kleiman

Active learning-guided optimization of cell-free biosensors for lead testing in drinking water

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.20.671382

N/A

0DataRank · unranked

1 citations

Nicole Chiang, Holly M. Ekas, Dylan M. Brown, Garrett Dildine, Tyler Lucci +8 more

Mechanistic basis for enhanced strigolactone sensitivity in KAI2 triple mutant

Biophysical Journal(2025)10.1016/j.bpj.2025.04.021

N/A

0DataRank · unranked

0 citations

Jiming Chen, Tanner J. Dean, Diwakar Shukla, Briana L. Sobecks

Multiple modes of cholesterol translocation in the human Smoothened receptor

eLife(2025)10.7554/elife.108030.1

N/A

0DataRank · unranked

0 citations

Maia Kinnebrew, Rajat Rohatgi, Diwakar Shukla, Prateek D. Bansal

Multiple modes of cholesterol translocation in the human Smoothened receptor

eLife(2025)10.7554/elife.108030

N/A

0DataRank · unranked

0 citations

Maia Kinnebrew, Rajat Rohatgi, Diwakar Shukla, Prateek D. Bansal

Role of substrate recognition in modulating strigolactone receptor selectivity in witchweed

Journal of Biological Chemistry(2021)10.1016/j.jbc.2021.101092

N/A

0DataRank · unranked

41 citations

Alexandra R.F. White, David C. Nelson, Diwakar Shukla, Jiming Chen

Investigation of gating in outer membrane porins provides new perspectives on antibiotic resistance mechanisms

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.09.459668

N/A

0DataRank · unranked

4 citations

Nandan Haloi, Rebecca J. Ulrich, Mary Elizabeth Metcalf, Po‐Chao Wen, William W. Metcalf +4 more

Engineered High-Affinity ACE2 Peptide Mitigates ARDS and Death Induced by Multiple SARS-CoV-2 Variants

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.21.473668

N/A

0DataRank · unranked

3 citations

Soumajit Dutta, Shiqin Xiong, Matthew C. Chan, Kui K. Chan, Timothy M. Fan +10 more

Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.22.473902

N/A

0DataRank · unranked

2 citations

Kui K. Chan, Erik Procko, Diwakar Shukla, Matthew C. Chan

Dual role of strigolactone receptor signaling partner in inhibiting substrate hydrolysis

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.01.470725

N/A

0DataRank · unranked

0 citations

Jiming Chen, Diwakar Shukla, Briana L. Sobecks

Engineered ACE2 decoy mitigates lung injury and death induced by SARS-CoV-2 variants

Nature Chemical Biology(2022)10.1038/s41589-021-00965-6

N/A

0DataRank · unranked

89 citations

Soumajit Dutta, Shiqin Xiong, Matthew C. Chan, Kui K. Chan, Timothy M. Fan +10 more

Contribution of Signaling Partner Association to Strigolactone Receptor Selectivity

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.21.500684

N/A

0DataRank · unranked

0 citations

Diwakar Shukla, Jiming Chen

Sequence basis for selectivity of ephrin-B2 ligand for Eph receptors and pathogenic henipavirus G glycoproteins

Journal of Virology(2023)10.1128/jvi.00621-23

N/A

0DataRank · unranked

9 citations

Moushimi Amaya, Natalie Tsang, Randy Yin, Alka Jays, Christopher C. Broder +3 more

Effect of histidine covalent modification on strigolactone receptor activation and selectivity

Biophysical Journal(2023)10.1016/j.bpj.2023.02.012

N/A

0DataRank · unranked

3 citations

Diwakar Shukla, Jiming Chen

Mechanistic Basis for Enhanced Strigolactone Sensitivity in KAI2 Triple Mutant

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.18.524622

N/A

0DataRank · unranked

1 citations

Jiming Chen, Tanner J. Dean, Diwakar Shukla, Briana L. Sobecks

The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.26.538420

N/A

0DataRank · unranked

0 citations

Moushimi Amaya, Natalie Tsang, Randy Yin, Alka Jays, Christopher C. Broder +3 more

Functional regulation of aquaporin dynamics by lipid bilayer composition

Nature Communications(2024)10.1038/s41467-024-46027-y

N/A

0DataRank · unranked

18 citations

Austin T. Weigle, Diwakar Shukla, Anh T. P. Nguyen

Substrate prediction for RiPP biosynthetic enzymes via masked language modeling and transfer learning

Digital Discovery(2024)10.1039/d4dd00170b

N/A

0DataRank · unranked

4 citations

Xuenan Mi, Douglas A. Mitchell, Diwakar Shukla, Joseph D. Clark

Molecular insights into the elevator-type mechanism of the cyanobacterial bicarbonate transporter BicA

Biophysical Journal(2024)10.1016/j.bpj.2024.12.013

N/A

0DataRank · unranked

4 citations

Yazeed Alfawaz, Arnav Paul, Diwakar Shukla, Matthew C. Chan