Computational Structural Biology Lab

Department of Biotechnology
Indian Institute of Technology Kharagpur

Total of 50 research articles and one book chapter are published in international peer reviewed journals with
  • Cumulative publication impact factor of ~166
  • Overall citation: 2537
  • H-index: 19
  • i10-index: 26
  • Articles

    1. A structure-based model for the prediction of protein-RNA binding affinity. Nithin C, Mukherjee S & Bahadur RP. RNA 2019 (accepted).
    2. 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.
    3. 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.
    4. 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;
    5. An account of solvent accessibility in protein-RNA recognition. Mukherjee S & Bahadur RP. Sci Rep 2018; 8:10546.
    6. 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.
    7. Effect of neighboring residues in conformational plasticity of Intrinsically disordered proteins. Basu S & Bahadur RP. Biophys J 2018; 114:588a
    8. 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.
    9. Genome-wide identification of miRNAs and lncRNAs in Cajanus cajan. Nithin C, Thomas A, Basak J & Bahadur RP. BMC Genomics 2017;18(1):878.
    10. A molecular dissection of non-host resistance in plants. Roy Chowdhury M, Bahadur RP & Basak J. Res J Biotech 2017;12(10):63-73.
    11. A non-redundant protein-RNA docking benchmark version 2.0. Nithin C, Mukherjee S & Bahadur RP. Proteins 2017; 85(2):256–267.
    12. 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
    13. A structural perspective of RNA recognition by intrinsically disordered proteins. Basu S & Bahadur RP. Cell Mol Life Sci 2016; 73(21):4075-4084.
    14. 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.
    15. Layers: A molecular surface peeling algorithm and its applications to analyze protein structure. Karampudi NBR and Bahadur RP. Sci Rep 2015; 5:16141.
    16. 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.
    17. 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.
    18. Molecular architecture of protein-RNA recognition sites. Barik A, C N, Pilla SP & Bahadur RP. J Biomol Struct Dyn 2015; 33(12):2738-51.
    19. Hydration of protein-RNA recognition sites. Barik A & Bahadur RP. Nucleic Acid Res.2014; 42(15):10148-60.
    20. 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.
    21. Protein-DNA docking with a coarse-grained force field. Setny P,Bahadur RP & Zacharias M. BMC Bioinformatics 2012;13:228.
    22. 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.
    23. A protein–RNA docking benchmark (I): Nonredundant cases. Barik A, Nithin C, Manasa P & Bahadur RP. Proteins 2012; 80:1866-1871.
    24. 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.
    25. 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.
    26. 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.
    27. 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.
    28. 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.
    29. 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.
    30. 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.
    31. Protein-protein interaction and quaternary structure. Janin J, Bahadur RP & Chakrabarti P. Quart. Rev. Biophys. 2008; 41:133-180.
    32. The structural basis of protein-nucleic acid recognition. Janin J and Bahadur RP. Cellular and Molecular Bioengineering. 2008; 1:327-338.
    33. Dissecting protein-RNA recognition sites. Bahadur RP, Zacharias M & Janin J. Nuc. Acids. Res. 2008; 36:2705-2716.
    34. 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.
    35. Residue conservation in virus capsid assembly. Bahadur RP & Janin J. Proteins 2008; 71:407-414.
    36. 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.
    37. 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.
    38. A dissection of the protein-protein interfaces in icosahedral virus capsids. Bahadur RP, Rodier F & Janin J. J. Mol. Biol. 2007; 367: 574-590.
    39. Macromolecular recognition in the Protein Data Bank. Janin J, Rodier F, Chakrabarti P & Bahadur RP. Acta. Crystallogr. D Biol. Crystallogr. 2007; D63: 1-8.
    40. 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).
    41. Revisiting the Voronoi description of protein-protein interfaces. Cazals F, Proust F, Bahadur RP & Janin J. Protein Sci. 2006; 15: 2082-2092.
    42. 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.
    43. 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.
    44. 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.
    45. Hydration of protein-protein interfaces. Rodier F, Bahadur RP, Chakrabarti P & Janin J. Proteins 2005; 60:36-45. (cover illustration).
    46. Residue contacts in protein structures and interfaces. Saha RP, Bahadur RP & Chakrabarti P. FEBS Journal 2005; 272:114.
    47. 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.
    48. Dissecting interfaces in protein-protein complexes and in homodimers. Janin J, Rodier F, Bahadur RP & Chakrabarti P. European Biophysics Journal 2003; 32:300.
    49. Dissecting subunit interfaces in homodimeric proteins. Bahadur RP, Chakrabarti P, Rodier F & Janin J. Proteins 2003; 53:708-719.
    50. 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).