Metadata
Title
Computational Structural Biology Lab
Category
general
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f3e1916b04d24355a3e1f09c54c73f63
Source URL
http://www.csb.iitkgp.ac.in/pages/publications.php
Parent URL
http://www.csb.iitkgp.ac.in/
Crawl Time
2026-03-18T08:11:08+00:00
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# Computational Structural Biology Lab

**Source**: http://www.csb.iitkgp.ac.in/pages/publications.php
**Parent**: http://www.csb.iitkgp.ac.in/

### Department of Biotechnology Indian Institute of Technology Kharagpur

- [Home](http://www.csb.iitkgp.ac.in/)
- [Research](http://www.csb.iitkgp.ac.in/pages/research.php)
- [Publications](http://www.csb.iitkgp.ac.in/pages/publications.php)
- [Teaching](http://www.csb.iitkgp.ac.in/pages/teaching.php)
- Tutorials
  - [Python Tutorial](http://www.csb.iitkgp.ac.in/tutorials/python/python_index.php)
  - [Gromacs Tutorial](http://www.csb.iitkgp.ac.in/tutorials/gromacs/gromacs_index.php)
- Tools
  - [PRince](http://www.facweb.iitkgp.ac.in/~rbahadur/prince/home.html)
  - [Layers](http://www.csb.iitkgp.ac.in/applications/mol_layers/main.php)
  - [HotSPRing](http://www.csb.iitkgp.ac.in/applications/HotSPRing/main.php)
  - [B-Cell epitope prediction](http://www.csb.iitkgp.ac.in/applications/b_cell_epitope_pred/main.php)
  - [NCodR](http://www.csb.iitkgp.ac.in/applications/NCodR/index.php)
  - [Nucpred](http://www.csb.iitkgp.ac.in/applications/Nucpred/index.php)
  - [proRBR](http://www.csb.iitkgp.ac.in/applications/proRBR/index.php)
  - [Rotamers for RBPs](http://www.csb.iitkgp.ac.in/applications/RBP-Rotamer/rotamer)
- Databases
  - [Protein folding similarity](#)
  - [miR\_database](http://www.csb.iitkgp.ac.in/databases/miR_details/index.php)
- Benchmarks
  - [Protein-RNA Docking Benchmark version 3](http://www.csb.iitkgp.ac.in/applications/PRDBv3/PRDBv3.php)
  - [Protein-RNA Docking Benchmark version 2](http://www.csb.iitkgp.ac.in/applications/PRDBv2.php)
  - [Protein-RNA Docking Benchmark version 1](http://www.csb.iitkgp.ac.in/applications/benchmark.php)
  - [Protein-RNA Affinity Benchmark](http://www.csb.iitkgp.ac.in/applications/affinity.php)
  - [ProRBR Dataset](http://www.csb.iitkgp.ac.in/applications/proRBR_dataset/proRBR)
- [Members](http://www.csb.iitkgp.ac.in/pages/members.php)
- Links
  - [Bioinformatics Centre](http://www.csb.iitkgp.ac.in/bioinformatics_centre/index.html)
  - [Homepage IITKGP](http://www.iitkgp.ac.in)
  - [Homepage Department of Bioscience and
    Biotechnology](http://www.bt.iitkgp.ac.in)
- [Contact](http://www.csb.iitkgp.ac.in/pages/contact.php)

- 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).