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Sunandan Mukherjee
Sunandan Mukherjee
International Institute of Molecular and Cell Biology in Warsaw, Poland
Verified email at iimcb.gov.pl - Homepage
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Cited by
Cited by
Year
MODOMICS: a database of RNA modification pathways. 2021 update
P Boccaletto, F Stefaniak, A Ray, A Cappannini, S Mukherjee, E Purta, ...
Nucleic Acids Research 50 (D1), D231–D235, 2022
4332022
QRNAS: software tool for refinement of nucleic acid structures
J Stasiewicz, S Mukherjee, C Nithin, JM Bujnicki
BMC Structural Biology 19 (1), 2019
572019
Computational modeling of RNA 3D structure based on experimental data
A Ponce-Salvatierra, Astha, K Merdas, C Nithin, P Ghosh, S Mukherjee, ...
Bioscience reports 39 (2), BSR20180430, 2019
402019
Probing binding hot spots at protein–RNA recognition sites
A Barik, C Nithin, NBR Karampudi, S Mukherjee, RP Bahadur
Nucleic Acids Research 44 (2), e9-e9, 2016
372016
A non‐redundant protein–RNA docking benchmark version 2.0
C Nithin, S Mukherjee, RP Bahadur
Proteins: Structure, Function, and Bioinformatics 85 (2), 256-267, 2017
342017
An account of solvent accessibility in protein-RNA recognition
S Mukherjee, RP Bahadur
Scientific Reports 8 (1), 10546, 2018
312018
MODOMICS: a database of RNA modifications and related information. 2023 update
A Cappannini, A Ray, E Purta, S Mukherjee, P Boccaletto, SN Moafinejad, ...
Nucleic Acids Research 52 (D1, 5), D239–D244, 2024
162024
Modeling of three-dimensional RNA structures using SimRNA
TK Wirecki, C Nithin, S Mukherjee, JM Bujnicki, MJ Boniecki
Protein Structure Prediction, 103-125, 2020
162020
Constrained peptides mimic a viral suppressor of RNA silencing
A Kuepper, N McLoughlin, S Neubacher, A Yeste-Vázquez, ...
Nucleic Acids Research 49 (22), 12622–12633, 2021
142021
Computational pipeline for reference-free comparative analysis of RNA 3D structures applied to SARS-CoV-2 UTR models
J Gumna, M Antczak, RW Adamiak, JM Bujnicki, SJ Chen, F Ding, ...
International Journal of Molecular Sciences 23 (17), 9630, 2022
12*2022
A structure-based model for the prediction of protein–RNA binding affinity
C Nithin, S Mukherjee, RP Bahadur
RNA 25 (12), 1628-1645, 2019
112019
NACDDB: Nucleic Acid Circular Dichroism Database
A Cappannini, K Mosca, S Mukherjee, SN Moafinejad, RR Sinden, ...
Nucleic Acids Research 51 (D1), D226–D231, 2023
92023
Dissecting water binding sites at protein–protein interfaces: a lesson from the atomic structures in the Protein Data Bank
S Mukherjee, C Nithin, Y Divakaruni, RP Bahadur
Journal of Biomolecular Structure and Dynamics 37 (5), 1204-1219, 2019
72019
RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints
G Chojnowski, R Zaborowski, M Magnus, S Mukherjee, JM Bujnicki
Bioinformatics 39 (9), btad527, 2023
6*2023
Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence
X Jia, Z Pan, Y Yuan, B Luo, Y Luo, S Mukherjee, G Jia, L Liu, X Ling, ...
Cell Research, 2023
52023
Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing
B Luo, C Zhang, X Ling, S Mukherjee, G Jia, J Xie, X Jia, L Liu, EF Baulin, ...
Nature Catalysis, 2023
42023
RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints
EF Baulin, S Mukherjee, SN Moafinejad, TK Wirecki, NG Badepally, ...
Proteins: Structure, Function, and Bioinformatics 91 (12), 1800-1810, 2023
32023
NCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae
C Nithin, S Mukherjee, J Basak, RP Bahadur
Quantitative Plant Biology 3, e23, 2022
32022
Residues at the interface between zinc binding and winged helix domains of human RECQ1 play a significant role in DNA strand annealing activity
S Mukhopadhyay, T Das, M Bose, CK Jain, M Chakraborty, S Mukherjee, ...
Nucleic Acids Research 49 (20), 11834-11854, 2021
32021
Discovery of a Trefoil Knot in the RydC RNA: Challenging Previous Notions of RNA Topology
W Niemyska, S Mukherjee, B Gren, S Niewieczerzal, JM Bujnicki, ...
Journal of Molecular Biology, 2024
22024
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