Computational Structural Biology Lab

Department of Biotechnology
Indian Institute of Technology Kharagpur

  • Overall citation: 4055
  • H-index: 28
  • i10-index: 43

    • Articles

    1. MetIoR: A meta predictor to predict intrinsic disorder in RNA binding proteins. Mitra, S., & Bahadur, R. P. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 2025; doi.org/10.1016/j.bbapap.2025.141119.
    2. LncRNA CASC19 promotes pancreatic cancer progression by increasing PSPC1 protein stability and facilitating the oncogenic PSPC1/ β-Catenin pathway. Moumita Mukherjee1, Swati Ghosh, Atanu Maity, Sukanta Ray, Hemabha Saha, Ranjit Prasad Bahadur & Srikanta Goswami. Molecular Medicine 2025; doi.org/10.1186/s10020-025-01363-7.
    3. Elucidating role of long non-coding RNAs of Tamarindus indica Linn. in post-transcriptional gene regulation. Roy Chowdhury Moumita, Kumar Aman ,Besra Alfred ,Bahadur R. P., & Basak Jolly. Plant Science today 2025; doi.org/10.14719/pst.3057
    4. Protein-RNA Docking Benchmark v3.0 Integrated With Binding Affinity. Shri Kant, Nithin C., Mukherjee S., Maity A., & Bahadur R. P. Proteins: Structure, Function, and Bioinformatics 2025; doi.org/10.1002/prot.26825.
    5. Allostery and inter-domain dynamics in NXF1: An insight into viral CTE-RNA binding. Chatterjee S., Maity A., & Bahadur R. P. International Journal of Biological Macromolecules. 2025; doi.org/10.1016/j.ijbiomac.2025.141374.
    6. pmiRScan: a LightGBM based method for prediction of animal pre-miRNAs. Venkatesan, A., Basak, J., & Bahadur, R. P. Functional & Integrative Genomics. 2025; DOI: 10.1007/s10142-025-01527-y.
    7. Conformational switches in human RNA binding proteins involved in neurodegeneration. Chatterjee, S., Maity, A., & Bahadur, R. P. Biochimica et Biophysica Acta (BBA)-General Subjects. 2025; doi.org/10.1016/j.bbagen.2025.130760.
    8. Efficient mapping of RNA-binding residues in RNA-binding proteins using local sequence features of binding site residues in protein-RNA complexes. Agarwal A, Kant S & Bahadur RP. Proteins. 2023; doi.org/10.1002/prot.26528.
    9. Modular architecture and functional annotation of human RNA-binding proteins containing RNA recognition motif. Agarwal A & Bahadur RP. Biochimie. 2023; doi.org/10.1016/j.biochi.2023.01.017.
    10. NCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae. Nithin C, Mukherjee S, Basak J & Bahadur RP. Quantitative Plant Biology. 2022; doi:10.1017/qpb.2022.18.
    11. A comparative analysis of machine learning classifiers for predicting protein-binding nucleotides in RNA sequences. Agarwal A, Kunal S, Kant S & Bahadur RP. Computational and Structural Biotechnology Journal. 2022; doi:10.1016/j.csbj.2022.06.036.
    12. Molecular insights into binding dynamics of tandem RNA recognition motifs (tRRMs) of human antigen R (HuR) with mRNA and the effect of point mutations in impaired HuR-mRNA recognition. Agarwal A, Alagar S, Kant S & Bahadur RP. Journal of Biomolecular Structure and Dynamics. 2022; doi:10.1080/07391102.2022.2073270.
    13. Impaired nuclear transport induced by juvenile ALS causing P525L mutation in NLS domain of FUS: A molecular mechanistic study. Basu S, Rajendra KC, Alagar S & Bahadur RP. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 2022; doi:10.1016/j.bbapap.2022.140766.
    14. Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins. Basu S & Bahadur RP. Proteins. 2021; doi:10.1002/prot.26261.
    15. Genome-wide prediction of cauliflower miRNAs and lncRNAs and their roles in post-transcriptional gene regulation. Chowdhury MR, Bahadur RP & Basak J. Planta. 2021; doi:10.1007/s00425-021-03689-y.
    16. Unusual RNA binding of FUS RRM studied by molecular dynamics simulation and enhanced sampling method. Basu S, Alagar S & Bahadur RP. Biophys. J. 2021; doi:10.1016/j.bpj.2021.03.001.
    17. DSS1 allosterically regulates the conformation of the tower domain of BRCA2 that has dsDNA binding specificity for homologous recombination. Alagar S & Bahadur RP. Int J Biol. Macromol. 2020; 165:918-929.
    18. Elucidating the functional role of predicted miRNAs in post-transcriptional gene regulation along with symbiosis in Medicago truncatula.Roy Chowdhury M, Basak J & Bahadur RP. Curr Bioinfo 2020; doi:10.2174/1574893614666191003114202.
    19. Do sequence neighbours of intrinsically disordered regions promote structural flexibility in intrinsically disordered proteins? Basu S & Bahadur RP. J Struct Biol 2019; doi:10.1016/j.jsb.2019.107428.
    20. Residue conservation elucidates the evolution of r-proteins in ribosomal assembly and function. Pilla SP & Bahadur RP. Int J Biol. Macromol. 2019; doi: 10.1016/j.ijbiomac.2019.08.127.
    21. A structure-based model for the prediction of protein-RNA binding affinity. Nithin C, Mukherjee S & Bahadur RP. RNA 2019; doi: 10.1261/rna.071779.119.
    22. Dissecting macromolecular recognition sites in ribosome: implication to its self-assembly. Pilla SP, Thomas A & Bahadur RP. RNA Biology 2019; doi:10. 1080/15476286.2019.1629767.
    23. Dissecting protein-protein interactions in proteasome assembly: implication to its self assembly. Pilla SP, Babu R & Bahadur RP. J Mol Recogn 2019; doi: 10.1002/jmr.2784.
    24. Identifcation and characterization of differentially expressed Phaseolus vulgaris miRNAs and their targets during mungbean yellow mosaic India virus infection reveals new insight into Phaseolus-MYMIV interaction. Patwa N, Nithin C , Bahadur RP & Basak J. Genomics 2018; doi.org/10.1016/j.ygeno.2018.09.005
    25. An account of solvent accessibility in protein-RNA recognition. Mukherjee S & Bahadur RP. Sci Rep 2018; 8:10546.
    26. Dissecting water binding sites at protein-protein interfaces: A lesson from the atomic structures in the Protein Data Bank. Mukherjee S, Nithin C, Divakaruni Y & Bahadur RP. J Biomol Struct Dyn. 2018; doi:10.1080/07391102.2018.1453379.
    27. Effect of neighboring residues in conformational plasticity of Intrinsically disordered proteins. Basu S & Bahadur RP. Biophys J 2018; 114:588a
    28. A machine learning approach towards sequence based RNA binding protein sites prediction in human proteome. Agarwal A, Sivanandan S, Mukherjee S, Chandran N & Bahadur, RP. FEBS Open Bio. 2018, 8:455.
    29. Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan. Nithin C, Thomas A, Basak J & Bahadur RP. BMC Genomics 2017;18(1):878.
    30. A molecular dissection of non-host resistance in plants. Roy Chowdhury M, Bahadur RP & Basak J. Res J Biotech 2017;12(10):63-73.
    31. A non-redundant protein-RNA docking benchmark version 2.0. Nithin C, Mukherjee S & Bahadur RP. Proteins 2017; 85(2):256–267.
    32. Influence of polymorphic conformations of DSS1 on its binding with BRCA2. Karampudi NBR, Das SB and Bahadur RP. Eur Biophys J with Biophys Lett 2017; 46:S219
    33. A structural perspective of RNA recognition by intrinsically disordered proteins. Basu S & Bahadur RP. Cell Mol Life Sci 2016; 73(21):4075-4084.
    34. Probing binding hot spots at protein-RNA recognition sites. Barik A, Nithin C, Karampudi NBR, Mukherjee S & Bahadur RP. Nucleic Acid Res 2016; 44(2):e9.
    35. Layers: A molecular surface peeling algorithm and its applications to analyze protein structure. Karampudi NBR and Bahadur RP. Sci Rep 2015; 5:16141.
    36. Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures. Nithin C, Patwa N, Thomas A, Bahadur RP & Basak J. BMC Plant Biol. 2015; 15:140.
    37. A repressor activator protein1 homologue from an oleaginous strain of Candida tropicalis increases storage lipid production in Saccharomyces cerevisiae. Chattopadhyay A, Dey P, Barik A, Bahadur RP & Maiti MK. FEMS Yeast Res.2015; 15(4):fov013.
    38. Molecular architecture of protein-RNA recognition sites. Barik A, C N, Pilla SP & Bahadur RP. J Biomol Struct Dyn 2015; 33(12):2738-51.
    39. Hydration of protein-RNA recognition sites. Barik A & Bahadur RP. Nucleic Acid Res.2014; 42(15):10148-60.
    40. Molecular modeling of protein-protein interaction to decipher the structural mechanism of nonhost resistance in Rice. Bahadur RP & Basak J. J of Biomol Struct Dyn.2014; 32(4):669-81.
    41. Protein-DNA docking with a coarse-grained force field. Setny P,Bahadur RP & Zacharias M. BMC Bioinformatics 2012;13:228.
    42. PRince: a web server for structural and physicochemical analysis of Protein-RNA interface. Barik A, Mishra A & Bahadur RP. Nucl Acids Res. 2012; 40:W440-W444.
    43. A protein–RNA docking benchmark (I): Nonredundant cases. Barik A, Nithin C, Manasa P & Bahadur RP. Proteins 2012; 80:1866-1871.
    44. The DNA-binding activity of an AP2 protein is involved in transcriptional regulation of a stress-responsive gene, SiWD40, in foxtail millet. Mishra AK, Puranik S, Bahadur RP & Prasad M. Genomics 2012;PMID:22771384.
    45. Biomt_dBase: A Database on Biomaterials. Subia B, Mukherjee S, Bahadur RP, Correlo VM, Reis, Rui L, Sabarinathan R, Sekar K & Kundu SC. Open Tissue Eng. Regen. Med. J. 2012; 5:9-16.
    46. Association of SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet (Setaria italica L.). Lata C, Bhutty S, Bahadur RP, Majee M & Prasad M. J. Exp. Botany. 2011; 62:3387-3401.
    47. Molecular cloning and characterization of a novel membrane associated NAC family gene, SiNAC from foxtail millet [Setaria italica (L.) P. Beauv.]. Puranik S, Bahadur RP, Srivastava PS & Prasad M. Molecular Biotechnol. 2011; 49(2):138-50.
    48. Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations. Bahadur RP, Kannan S & ZachariasM. Biophys. J. 2009; 97:3139-3149.
    49. Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins. Bahadur RP & Chakrabarti P. BMC Structural Biology 2009; 9:76-84.
    50. Accessibilities and partner number of protein residues, their relationship and a web server, ContPlot for their display. Pal A, Bahadur, RP, Ray PS, & Chakrabarti P. BMC Bioinformatics. 2009; 10:103-112.
    51. Protein-protein interaction and quaternary structure. Janin J, Bahadur RP & Chakrabarti P. Quart. Rev. Biophys. 2008; 41:133-180.
    52. The structural basis of protein-nucleic acid recognition. Janin J and Bahadur RP. Cellular and Molecular Bioengineering. 2008; 1:327-338.
    53. Dissecting protein-RNA recognition sites. Bahadur RP, Zacharias M & Janin J. Nuc. Acids. Res. 2008; 36:2705-2716.
    54. The Interface of Protein-Protein Complexes: Analysis of Contacts and Prediction of Interactions. Bahadur RP & Zacharias M. Cell. Mol. Life Sci. 2008; 65:1059-1072.
    55. Residue conservation in virus capsid assembly. Bahadur RP & Janin J. Proteins 2008; 71:407-414.
    56. DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions. Bernauer J, Bahadur RP, Rodier F, Janin J & Poupon A. Bioinformatics 2008; 24:652-658.
    57. A Knowledge-Based Potential for Protein-RNA Docking. Bahadur RP and Zacharias M. Publication Series of the John von Neumann Institute for Computing (NIC). NIC Series 2008; 40; 157-160.
    58. A dissection of the protein-protein interfaces in icosahedral virus capsids. Bahadur RP, Rodier F & Janin J. J. Mol. Biol. 2007; 367: 574-590.
    59. Macromolecular recognition in the Protein Data Bank. Janin J, Rodier F, Chakrabarti P & Bahadur RP. Acta. Crystallogr. D Biol. Crystallogr. 2007; D63: 1-8.
    60. Peptide segments in Protein-Protein Interfaces. Pal A, Chakrabarti P, Bahadur RP, Rodier F & Janin J. Journal of Biosciences 2007; 32:101-111. (cover illustration).
    61. Revisiting the Voronoi description of protein-protein interfaces. Cazals F, Proust F, Bahadur RP & Janin J. Protein Sci. 2006; 15: 2082-2092.
    62. Theoretical model of the three-dimensional structure of a disease resistance gene homolog encoding resistance protein in Vigna mungo. Basak J & Bahadur RP. J. Biomol. Struct. Dyn. 2006; 24: 123-130.
    63. PRO_FACE: a server for the analysis of the physicochemical features of protein-protein interfaces. Saha RP, Bahadur RP, Pal A, Mandal S & Chakrabarti P. BMC Structural Biology 2006; 6:11, 1-5.
    64. Interresidue contacts in proteins and protein-protein interfaces and their use in characterizing the homodimer interface. Saha RP, Bahadur RP & Chakrabarti P. J. Proteome Res. 2005; 4:1600-1609.
    65. Hydration of protein-protein interfaces. Rodier F, Bahadur RP, Chakrabarti P & Janin J. Proteins 2005; 60:36-45. (cover illustration).
    66. Residue contacts in protein structures and interfaces. Saha RP, Bahadur RP & Chakrabarti P. FEBS Journal 2005; 272:114.
    67. A dissection of specific and non-specific protein-protein interfaces. Bahadur RP, Chakrabarti P, Rodier F & Janin J. J. Mol. Biol. 2004; 336:943-955.
    68. Dissecting interfaces in protein-protein complexes and in homodimers. Janin J, Rodier F, Bahadur RP & Chakrabarti P. European Biophysics Journal 2003; 32:300.
    69. Dissecting subunit interfaces in homodimeric proteins. Bahadur RP, Chakrabarti P, Rodier F & Janin J. Proteins 2003; 53:708-719.
    70. Quantifying the accessible surface area of protein residues in their local environment. Samanta U, Bahadur RP & Chakrabarti P. Protein Engng. 2002; 15:659-667.

    Book chapters

    1. A Structural perspective on protein-protein interactions in macromolecular assemblies. Bahadur RP. In "Protein-protein complexes: Analysis, Modeling and drug design". (Editor: M. Zacharias) Imperial College Press, London, UK. (2010).