A full list of publications can be found here
(First / corresponding author):
[1] Amrita, Chakraborti S, Dey S* (2024). Physicochemical features of subunit interfaces and their role in self-assembly across the ferritin superfamily. Structure (in press).
https://doi.org/10.1016/j.str.2024.12.004
[2] Tajane, S. V., Thakur, A., Acharya, S., Chakrabarti, P. & Dey, S* (2024). On the abundance and importance of AXXXA sequence motifs in globular proteins and their involvement in Cβ—Cβ interaction. J Struct Biol 216, 108129.
https://doi.org/10.1016/j.jsb.2024.108129
[3] Dhiman V, Marik D, Amrita, Shekhawat RS, Swain AK, Dey A, Yadav P*, Pal A*, Dey S*, Sadhukhan A* (2024). AP2/ERF Transcription Factor Orthologs of the Desert Tree Prosopis cineraria Show Higher Copy Number and DNA-Binding Affinity than Drought-Sensitive Species. J Plant Growth Regul.
https://doi.org/10.1007/s00344-024-11532-3
[4] Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S*, Levy ED* (2024). An atlas of protein homo-oligomerization across domains of life. Cell 187(4):999-1010.e15.
https://doi.org/10.1016/j.cell.2024.01.022
[5] Pal A, Chakrabarti P, Dey S* (2022) ProDFace: A web tool for the Dissection of Protein-DNA Interfaces. Front. Mol. Biosci. 9:978310.
https://doi.org/10.3389/fmolb.2022.978310
[6] Dey S, Prilusky J, Levy ED*. (2022) QSalignWeb: A Server to Predict and Analyze Protein Quaternary Structure. Front Mol Biosci. 8:787510.
https://doi.org/10.3389/fmolb.2021.787510
[7] Dey S*, Levy ED*. (2021) PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry. Structure, 29,1-9.
https://doi.org/10.1016/j.str.2021.07.012
[8] Dey S, Ritchie DW, Levy ED*. (2018) PDB-wide identification of biological assemblies from conserved quaternary structure geometry. Nature Methods 15(1):67-72. (F1000 recommended)
https://doi.org/10.1038/nmeth.4510
[9] Dey S, Pal A, Guharoy M, Sonavane S, Chakrabarti P*. (2012) Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining composition, conservation and structural parameters. Nucleic Acids Res. 40(15): 7150-7161.
https://doi.org/10.1093/nar/gks405
[10] Dey S, Chakrabarti P, Janin J*. (2011) A survey of hemoglobin quaternary structures. Proteins. 79(10):2861-2870.
https://doi.org/10.1002/prot.23112
[11] Dey S, Pal A, Chakrabarti P, Janin J* (2010). The Subunit Interfaces of Weakly Associated Homodimeric Proteins. J Mol Biol. 398:146-160.
https://doi.org/10.1016/j.jmb.2010.02.020
Middle authorship papers (in chronological order):
[12] Schweke et al. (2023) Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study. Proteomics. 23(17):e2200323.
https://doi.org/10.1002/pmic.202200323
[13] PDBe-KB consortium. (2022) PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50(D1):D534-D542.
https://doi.org/10.1093/nar/gkab988
[14] Varadi M et al. (2020) PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48(D1):D344-D353.
https://doi.org/10.1093/nar/gkz853
[15] Empereur-Mot C, Garcia-Seisdedos H, Elad N, Dey S, and Levy ED. (2019) Geometric description of self-interaction potential in symmetric protein complexes. Scientific Data. 6(1):64.
https://doi.org/10.1038/s41597-019-0058-x
[16] Ler LD et al. (2017) Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2. Science Translational Medicine. 22;9(378).
https://doi.org/10.1126/scitranslmed.aai8312
[17] Tan J et al. (2015) Genomic landscapes of breast fibroepithelial tumors. Nature Genetics 47(11):1341-5.
https://doi.org/10.1038/ng.3409
[18] Dasgupta B, Dey S, Chakrabarti P. (2014) Water and side-chain embedded π-turns. Biopolymers. 101 (5), 441-453.
https://doi.org/10.1002/bip.22401
[19] Chatterjee T, Pal A, Chakravarty D, Dey S, Saha RP, Chakrabarti P. (2013) Protein L-isoaspartyl-O-methyltransferase of Vibrio cholerae: Interaction with cofactors and effect of osmolytes on unfolding. Biochimie. 95(4):912-21.
https://doi.org/10.1016/j.biochi.2012.12.013
[20] Chatterjee T, Pal A, Dey S, Chatterjee BK, Chakrabarti P. (2012) Interaction of virstatin with human serum albumin: spectroscopic analysis and molecular modelling. PLoS One. 7(5):e37468.
https://doi.org/10.1371/journal.pone.0037468
[21] Mazumder A, Bandyopadhyay S, Dhar A, Lewis DE, Deb S, Dey S, Chakrabarti P, Roy S. (2012) A genetic network that balances two outcomes utilizes asymmetric recognition of operator sites. Biophys J. 102(7):1580-1589.
https://doi.org/10.1016/j.bpj.2012.01.052
[22] Chatterjee T, Mukherjee D, Dey S, Pal A, Hoque KM, Chakrabarti P. (2011) Accessory cholera enterotoxin, Ace,from Vibrio cholerae: structure, unfolding, and virstatin binding. Biochemistry. 50:2962-2972.
[23] Joshi P, Chakraborty S, Dey S, Shanker V, Ansari ZA, Singh SP, Chakrabarti P. (2011) Binding of chloroquine- conjugated gold nanoparticles with bovine serum albumin. J Colloid Interface Sci. 355:402-409.
https://doi.org/10.1016/j.jcis.2010.12.032
[24] Raychaudhuri S, Dey S, Bhattacharyya NP, Mukhopadhyay D. (2009) The role of intrinsically unstructured proteins in neurodegenerative diseases. PLoS One; 4(5):e5566.
https://doi.org/10.1371/journal.pone.0005566
Book Chapters:
[22] Dey S, Levy ED. (2018) Inferring and Using Protein Quaternary Structure Information from Crystallographic Data. Methods Molecular Biology, Vol. 1764: 357-375.
https://doi.org/10.1007/978-1-4939-7759-8_23