Publications

Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding
Salcedo, M.V., Gravel, N., Keshavarzi, A., Huang, L.C., Kochut, K.J. and Kannan, N.
PeerJ, 2023
Article DOI
Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases
Venkat, A., Watterson, G., Byrne, D.P., Boyle, B.O., Shrestha, S., Gravel, N., Fairweather, E.E., Daly, L.A., Bunn, C., Yeung, W., Aggarwal, I, Katiyar, S., Eyers, C.E., Eyers, P.A., and Kannan, N.
elife, 2023
Article DOI
Prevalence and Homology of the Pneumococcal Serine-Rich Repeat Protein at the Global Scale
Aceil, J., Venkat, A., Pan, E., Kannan, N. and Avci, F.
Microbiology Spectrum, 2023
Article DOI
Structural and biochemical insight into a modular β-1, 4-galactan synthase in plants
Prabhakar, P.K., Pereira, J.H., Taujale, R., Shao, W., Bharadwaj, V.S., Chapla, D., Yang, J.Y., Bomble, Y.J., Moremen, K.W., Kannan, N., Hammel, M., Adams, P.D., Scheller, H.V., and Urbanowicz, B.R.
Nature Plants, 2023
Article DOI
Phosformer: an explainable transformer model for protein kinase-specific phosphorylation predictions
Zhou, Z., Yeung, W., Gravel, N., Salcedo, M., Soleymani, S., Li, S. and Kannan, N.
Bioinformatics, 2023
Article DOI
Evolutionary and cellular analysis of the ‘dark’pseudokinase PSKH2
Byrne, D.P., Shrestha, S., Daly, L.A., Marensi, V., Ramakrishnan, K., Eyers, C.E., Kannan, N. and Eyers, P.A.
Biochemical Journal, 2023
Article DOI
Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies
Yeung, W., Zhou, Z., Mathew, L., Gravel, N., Taujale, R., O’Boyle, B., Salcedo, M., Venkat, A., Lanzilotta, W., Li, S. and Kannan, N.
Briefings in Bioinformatics, 2023
Article DOI
Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings
Yeung, W., Zhou, Z., Li, S. and Kannan, N.
Briefings in Bioinformatics, 2023
Article DOI
Protein kinase inhibitor selectivity “hinges” on evolution
Shrestha, S., Bendzunas, G. and Kannan, N.
Structure, 2022
Article DOI
Polymerization of the backbone of the pectic polysaccharide rhamnogalacturonan I
Amos, R.A., Atmodjo, M.A., Huang, C., Gao, Z., Venkat, A., Taujale, R., Kannan, N., Moremen, K.W. and Mohnen, D.
Nature Plants, 2022
Article DOI
Mutations in protein kinase Cγ promote spinocerebellar ataxia type 14 by impairing kinase autoinhibition
Pilo, C.A., Baffi, T.R., Kornev, A.P., Kunkel, M.T., Malfavon, M., Chen, D.H., Rossitto, L.A., Chen, D.X., Huang, L.C., Longman, C. and Kannan, N.
Science signaling, 2022
Article DOI
Modularity of the hydrophobic core and evolution of functional diversity in fold A glycosyltransferases.
Venkat, A., Tehrani, D., Taujale, R., Yeung, W., Gravel, N., Moremen, K.W. and Kannan, N.
The Journal of biological chemistry, 2022
Article DOI
Functional classification and validation of yeast prenylation motifs using machine learning and genetic reporters.
Berger, B.M., Yeung, W., Goyal, A., Zhou, Z., Hildebrandt, E.R., Kannan, N. and Schmidt, W.K.
PloS one, 2022
Article DOI
Computational tools and resources for pseudokinase research.
O'Boyle, B., Shrestha, S., Kochut, K., Eyers, P.A. and Kannan, N.
Methods in Enzymology, 2022
Article DOI
Target 2035-update on the quest for a probe for every protein.
Mueller, S., Ackloo, S., Al Chawaf, A., Al-Lazikani, B., Antolin, A., Baell, J. B., ... Kannan N, ... Arrowsmith, C. H.
RSC Medicinal Chemistry, 2022
Article DOI
Mapping the glycosyltransferase fold landscape using interpretable deep learning.
Taujale, R., Zhou, Z., Yeung, W., Moremen, K. W., Li, S., and Kannan N
Nature Communications, 2021
Article DOI
Evolution of Functional Diversity in the Holozoan Tyrosine Kinome.
Yeung, W., Kwon, A., Taujale, R., Bunn, C., Venkat, A., and Kannan N.
Molecular Biology and Evolution, 2021
Article DOI
GTXplorer: A portal to navigate and visualize the evolutionary information encoded in fold A glycosyltransferases.
Taujale, R., Soleymani, S., Priyadarshi, A., Venkat, A., Yeung, W., Kochut, K. J., and Kannan N.
Glycobiology, 2021
Article DOI
Peters plus syndrome mutations affect the function and stability of human beta 1,3-glucosyltransferase.
Zhang, A., Venkat, A., Taujale, R., Mull, J. L., Ito, A., Kannan N., and Haltiwanger, R. S.
Journal of Biological Chemistry
Article DOI
mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif.
Baffi, T. R., Lorden, G., Wozniak, J. M., Feichtner, A., Yeung, W., Kornev, A. P., ... Kannan N., ... Newton, A. C.
Science Signaling, 2021
Article DOI
Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis.
Garnish, S.E., Meng, Y., Koide, A., Sandow, J.J., Denbaum, E., Jacobsen, A.V., Yeung, W., Samson, A.L., Horne, C.R., ... Kannan, N. ... and Young, S.N.
Nature Communications, 2021
Article DOI
Granulovirus PK-1 kinase activity relies on a side-to-side dimerization mode centered on the regulatory αC helix.
Oliver, M.R., Horne, C.R., Shrestha, S., Keown, J.R., Liang, L.Y., Young, S.N., Sandow, J.J., Webb, A.I., Goldstone, D.C., Lucet, I.S. and Kannan, N.
Nature Communications, 2021
Article DOI
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases.
Huang, L.C., Taujale, R., Gravel, N., Venkat, A., Yeung, W., Byrne, D.P., Eyers, P.A. and Kannan, N.
BMC Bioinformatics, 2021
Article DOI
A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation.
Picado A, Chaikuad A, Wells CI, Shrestha S, Zuercher WJ, Pickett JE, Kwarcinski FE, Sinha P, de Silva CS, Zutshi R, Liu S, Kannan N, Knapp S, Drewry DH, Willson TM.
J Med Chem, 2020
Article DOI
Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction.
Huang LC, Yeung W, Wang Y, Cheng H, Venkat A, Li S, Ma P, Rasheed K, and Kannan N
BMC Bioinformatics, 2020
Article DOI
Google Scholar

Publications

Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding

Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases

Prevalence and Homology of the Pneumococcal Serine-Rich Repeat Protein at the Global Scale

Structural and biochemical insight into a modular β-1, 4-galactan synthase in plants

Phosformer: an explainable transformer model for protein kinase-specific phosphorylation predictions

Evolutionary and cellular analysis of the ‘dark’pseudokinase PSKH2

Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies

Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings

Protein kinase inhibitor selectivity “hinges” on evolution

Polymerization of the backbone of the pectic polysaccharide rhamnogalacturonan I

Mutations in protein kinase Cγ promote spinocerebellar ataxia type 14 by impairing kinase autoinhibition

Modularity of the hydrophobic core and evolution of functional diversity in fold A glycosyltransferases.

Functional classification and validation of yeast prenylation motifs using machine learning and genetic reporters.

Computational tools and resources for pseudokinase research.

Target 2035-update on the quest for a probe for every protein.

Mapping the glycosyltransferase fold landscape using interpretable deep learning.

Evolution of Functional Diversity in the Holozoan Tyrosine Kinome.

GTXplorer: A portal to navigate and visualize the evolutionary information encoded in fold A glycosyltransferases.

Peters plus syndrome mutations affect the function and stability of human beta 1,3-glucosyltransferase.

mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif.

Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis.

Granulovirus PK-1 kinase activity relies on a side-to-side dimerization mode centered on the regulatory αC helix.

KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases.

A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation.

Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction.