List of Publication



  1. S. Panigrahi, A. Bhattacharya, S. Banerjee, D. Bhattacharyya Interaction of Nucleobases with Wrinkled Graphene Surface: Dispersion Corrected DFT and AFM Studies. J. Phys. Chem. C (in press)

  2. M.K. Sarangi, D. Bhattacharyya, S. Basu (2012) Influence of 2'-Deoxy Sugar Moiety on Excited-State Protonation Equilibrium of Adenine and Adenosine with Acriding inside SDS Micelles: A Time-resolved Study with Quantum Chemical Calculations. ChemPhysChem. 13 525-534.

  3. M. Santosh, S. Panigrahi, D. Bhattacharyya, A.K. Sood, P. Maiti (2012) Unzipping and Binding of siRNA with Single Walled Carbon Nanotube: A Platform For siRNA Delivery. J. Chem. Phys. in press

  4. S. Panigrahi, A. Bhattacharya, D. Bandyopadhyay, S. J. Grabowski, D. Bhattacharyya, S. Banerjee (2011) Wetting Property of the Edges of Monoatomic Step on Graphite: Frictional-Force Microscopy and ab Initio Quantum Chemical Studies. J. Phys. Chem. C115,14819-14826.

  5. S. Panigrahi, R. Pal, D. Bhattacharyya (2011) Structure and Energy of Non-Canonical Base Pairs: Comparison of Various Computational Chemistry Methods with Crystallographic Ensembles. J. Biomol. Struct. Dynam. 29, 541-556.

  6. S. Basu, D. Bhattacharyya and R. Banerjee (2011) Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs., BMC Bioinformatics 12, 195.

  7. R.S.K. Vijayan, D. Bhattacharyya and N. Ghoshal (2011) Deciphering the binding mode of Zolpidem to GABAA α1 receptor – insights from molecular dynamics simulation, J. Mol. Model (in press)

  8. M. Chawla, P. Sharma, S. Halder, D. Bhattacharyya and A. Mitra (2011) Protomation of base pairs in RNA: Context Analysis and Quantum Chemical Investigations of their Geometries and Stabilities, J. Phys, Chem. B 115: 1469-1484

  9. S. Halder and D. Bhattacharyya(2010) Structural Stability of Tandemly Occurring Noncanonical Basepairs within Double Helical Fragments: Molecular Dynamics Studies of Functional RNA. J. Phys. Chem. B 114: 14028-14040.

  10. P. Sharma, J. Sponerova, J. Sponer, S. Sharma, D. Bhattacharyya and A. Mitra (2010) On the Role of cis Hoogsteen:Sugar Edge Family of Base Pairs in Platforms and Triplets – Quantum Chemical Insights into RNA Structural Biology. J. Phys. Chem. B 114: 3307-3320.

  11. N. M. Mascarenhas, D. Bhattacharyya and N. Ghoshal (2010) Why Pyridine Containing Pyrido[2,3-d]pyrimidin-7-ones Selectively Inhibit CDK4 Than CDK2: Insights From Molecular Dynamics Simulation. J. Molec. Graphics Modelling 28: 695-706.

  12. A. Borkar, I. Ghosh and D. Bhattacharyya (2010) Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace: A Molecular Mechanics Approach. J. Biomol. Struct. Dynam 27:695-712

  13. S. Samanta, J. Chakrabarti and D. Bhattacharyya (2010) Changes in Thermodynamic Properties of DNA Base Pairs in Protein-DNA Recognition. J. Biomol. Struct. Dynam. 27: 429-442

  14. V. Venugopal, A.K. Datta, D. Bhattacharyya, D. Dasgupta and R. Banerjee (2009)Structure of cyclophilin from Leishmania donovani bound to cyclosporin at 2.6 A resolution: correlation between structure and thermodynamic data. Acta Cryst. D 65: 1187-1195

  15. S. Samanta, S. Mukherjee, J. Chakrabarti, and D. Bhattacharyya (2009) Structural properties of polymeric DNA from molecular dynamics simulations. J. Chem. Phys 130:115103.

  16. A. Mladek, P. Sharma, A. Mitra, D. Bhattacharyya, J. Sponer and J.E. Sponer (2008) The Trans Hoogsteen/Sugar Edge Base Pairing in RNA. Structures, Energies and Stabilities from Quantum Chemical Calculations. J. Phys. Chem. B 113:1743-1755 .

  17. J. Basu, D. Bhattacharyya and B. Sarkar (2008) Overall Cluster Effectiveness Index: An Instrument for Assessment of Development Programs for Industrial Clusters in Developing Countries., Sedme journal 35: 70-94

  18. P. Sharma, A. Mitra, S. Sarma, H. Singh, D. Bhattacharyya (2008) Quantum Chemical Studies of Structures and Binding in Noncanonical RNA Base Pairs: The Trans Watson-Crick:Watson-Crick Family. J. Biomol. Struct. Dynam. 25, 709-732.

  19. T. Sarkar, S. Roy, J. Bhattacharya, D. Bhattacharya, C.K. Mitra and A.K. Dasgupta (2008) Thermal Histerisis of some important physical properties of Nanoparticles, J. Colloid Interfac Sci. 327: 224-232

  20. S. Samanta, M. Kabir, B. Sanyal and D. Bhattacharyya (2008) Twist-Dependent Stacking Energy of Base-Pair Steps in B-DNA Geometry: A Density Functional Theory Approach, Int. J. Quant. Chem. 108: 1173-1180

  21. P. Sharma, A. Mitra, S. Sharma, H. Singh and D. Bhattacharyya (2008) Quantum Chemical Studies of Structures and binding in Noncanonical RNA Base pairs: The Trans Watson Crick/WatsonCrick family. J. Biomol. Struct. Dynam. 25: 709-732.

  22. A. Roy, S. Panigrahi, M. Bhattacharyya, and D. Bhattacharyya (2008) Structure, Stability, and Dynamics of Canonical and Noncanonical Base Pairs: Quantum Chemical Studies, J. Phys. Chem. B 112: 3786-3796

  23. S. Banerjee and D. Bhattacharyya (2008) Electronic properties of nano-graphene sheets calculated using quantum chemical DFT, Comput. Mater. Sci.doi: 10.1016/j.commatsci.2008.01.044

  24. D. Dey, A. Basu, D. Bhattacharyya, S. Basu, S.S. Maity and S. Ghosh (2007) Dibenzo[a,c]phenazine: A Polarity Insensitive Hydrogen Bonding Probe, J. Phys. Chem. A111, 10500-10506.

  25. D. Bhattacharyya, S.C. Koripella, A. Mitra, V.B. Rajendran and B. Sinha (2007) Theoretical Analysis of Noncanonical Base Pairing Interactions in RNA Molecules, J. Biosci. 32, 809-25.

  26. The NMITLI-BioSuite Team (2007) BioSuite: A comprehensive bioinformatics software package (A unique industry academia collaboration), Current Science, 92, 29-38.

  27. S. Mukherjee, M. Bansal and D. Bhattacharyya (2006) Conformational specificity of non-canonical base pairs 4 and higher order structures in nucleic acids: crystal 5 structure database analysis, J. Comp. Aided Mol. Des. 20, 629-45.

  28. J. Das, S. Mukherjee, A. Mitra and D. Bhattacharyya (2006) Non-Canonical Base Pairs and Higher Order Structures in Nucleic Acids: Crystal Structure Database Analysis J. Biomol. Struct. Dynam. 24, 149-161.

  29. D. Bandyopadhyay and D. Bhattacharyya (2006) Estimation of Strength in different Extra Watson-Crick Hydrogen Bonds in DNA Double Helices through Quantum Chemical studies, Biopolymers 83, 313-325.

  30. K. Sen, S. Basu and D. Bhattacharyya (2006) Ab Initio Studies on Excited State Intramolecular Electron Transfer in 4-Amino-/N/-Methylphthalimide and 3- Amino-/N/-Methylphthalimide Int. J. Quantum Chem. 106, 913-927.

  31. M.C. Blaise, D. Bhattacharyya, R. Sowdhamini and N. Pradan (2005) Structural consequences of D481N/K483Q mutation at glycine binding site of NMDA ionotropic glutamate receptors: a molecular dynamics study. J Biomol Struct Dynam. 22, 399-410.

  32. D. Bhattacharyya, K. Sen and S. Mukherjee (2005) Non-planar Amino Groups: Protein Structure Database Analysis and Ab Initio Quantum Chemical Studies on Model Systems Ind. J. Chem. A (Special Issue on Chemoinformatics and Computer Aided Drug Design) 45A, 58-67.

  33. S. Mukherjee, S. Majumdar and D. Bhattacharyya (2005) Role of Hydrogen Bonds in Protein-DNA Recognition: Effect of Non-planar Amino Groups, J. Phys. Chem. B 109, 10484-10492.

  34. S. Basu, R. Majumdar, G.K. Das and D. Bhattacharyya (2005) Energy Barriers and Rates of Tautomeric Transitions in DNA Bases: Ab initio Quantum Chemical Study Ind. J. Biochem. Biophys. 42, 378-385.

  35. S. Mukherjee and D. Bhattacharyya (2004) Effect of Phosphorothioate Chirality on the Grooves of DNA Double Helices: A Molecular Dynamics Study Biopolymers 73, 269-82.

  36. A.K. Dasgupta, R. Majumdar and D. Bhattacharyya (2004) Characterization of non-planar peptide groups in protein crystal structures Ind. J. Biochem. Biophys. 42, 49-55.

  37. K. Sen, S. Basu and D. Bhattacharyya (2004) QM/MM study of excited state electron transfer between pyrene and 4,4-Bis (dimethylamino)diphenylmethane with different solvent systems: role of hydrogen bonding within solvent molecules Inter. J. Quantum Chemistry 102, 368-378.

  38. S. K. Maji, D. Haldar, D. Bhattacharyya, A. Banerjee (2003) Conformational heterogeneity of a turn mimetic pseudo-peptide: comparison of crystal state, solution and theoretically derived structures J. Mol. Struct. 646, 111-123.

  39. D. Bandyopadhyay and D. Bhattacharyya (2003) Different Modes of Interaction between hydrated magnesium ion and DNA functional groups: Database analysis and ab initio studies J. Biomol. Struct. Dynam. 21, 447-458.

  40. R. Banerjee, M. Sen, D. Bhattacharya and P. Saha (2003) The Jigsaw Puzzle Model: Search for Conformational Specificity in Protein Interiors J. Mol. Biol. 333, 211-226.

  41. D. Bandyopadhyay and D. Bhattacharyya (2002) Effect of flanking residues on CA and AA dinucleotides: Some rationale J. Biomol. Struct. Dynam. 19, 659-667.

  42. S. Kundu, D. Bhattacharyya, R. Majumdar and A.R. Thakur (2001) Nucleosomal positioning and genetic divergence study based on DNA flexibility map J. Biomol. Struct. Dynam. 18, 527-533.

  43. K. Sen, S. Bandyopadhyay, D. Bhattacharyya and S. Basu (2001) Dielectric dependence of magnetic field effect: A tool for identification of exciplex and triplex J. Phys. Chem. 105, 9077-9084.

  44. S. Chakrabarti, D. Bhattacharyya, D. Dasgupta (2001) Structural basis of DNA recognition by anticancer antibiotics, chromomycin A(3), and mithramycin: roles of minor groove width and ligand flexibility. Biopolymers 56, 85-95.

  45. D. Bhattacharyya and R. Majumdar (2001) Structural basis of DNA flexibility Ind. J. Biochem. Biophys.37, 16-19.

  46. D. Bhattacharyya, G.K. Das and D.P. Burma (2001) Peptidyl transferase activity of RNA: A quantum chemical study Ind. J. Biochem. Biophys. 38, 48-52.

  47. Chakrabarti, D. Dasgupta and D. Bhattacharyya (2000) Role of Mg2+ in chromomycin A3-DNA interaction: A molecular modeling study J. Biol. Phys. 26, 203- 218.

  48. S. Chakrabarti, P. Aich, D. Sarker, D. Bhattacharyya, D. Dasgupta (2000) Role of Mg2+ in the interaction of anticancer antibiotic, chromomycin A3 with DNA: does neutral antibiotic bind DNA in absence of the metal ion? J Biomol. Struct. Dynam. 18, 209-218.

  49. Bandyopadhyay and D. Bhattacharyya (2000) Effect of neighboring residues in base-pair doublet geometry: A molecular dynamics study J. Biomol. Struct. Dynam. 18, 29-43.

  50. D. Bhattacharyya, S. Kundu, A.R. Thakur and R. Majumdar (1999) Sequence Directed Flexibility of DNA and the Role of Cross-strand Hydrogen Bonds J. Biomol. Struct. Dynam. 17, 289-300.

  51. K. Das, D. Bhattacharyya and D.P. Burma (1999) A Possible Mechanism of Peptide Bond Formation on Ribosome without Mediation of Peptidyl Transferase J. Theor. Biol. 200, 193-205.

  52. Banerjee, S. Ray and D. Bhattacharyya (1999) Surface Complementarity of Buried Protein Residues Current Science 78, 258-267.

  53. Majee, R. Sen, S. Guha, D. Bhattacharyya and D. Dasgupta (1997) Differential Interactions of the Mg2+ Complexes of Chromomycin A3 and Mithramycin with Poly(dG-dC).poly(dC-dG) and Poly(dG).Poly(dC) Biochemistry 36, 2291-2299.

  54. Bhattacharyya, B.R. Brooks and L. Callahan (1996) Positioning of Positively Charged Residues in the V3 Loop of HIV-1 GP120 Correlates with Syncytium Inducing Phenotype AIDS Res. Hum. Retrov. 12, 83-90.

  55. Bansal, D. Bhattacharyya and B. Ravi (1995) NUPARM and NUCGEN: Software for Analysis and Generation of Sequence Dependent Nucleic Acid Structures CABIOS 11, 281-287.

  56. Bansal, D. Bhattacharyya and S. Vijaylaksmi (1995) NUVIEW: Software for Display and Interactive Manipulation of Nucleic Acid Models CABIOS 11, 289-292.

  57. K. Nagaich, D. Bhattacharyya, S.K. Brahmachari and M. Bansal (1994) CA/TG Sequence at the 5'-end of Oligo A-Tracts Strongly Modulates DNA Curvature J. Biol. Chem. 269, 7824-7833.

  58. Bhattacharyya and M. Bansal (1994) Analysis of Base Sequence Dependent Variability in Secondary and Tertiary Structure of tRNA Molecules J. Biomol. Struct. Dynam. 11, 1251-1275.

  59. Bhattacharyya and M. Bansal (1992) Groove Width and Depths of B-DNA Structures Depend on Local Variation is Slide J. Biomol. Struct. Dynam.10, 213-226.

  60. Bansal, D. Bhattacharyya and D. Mohanty (1991) DNA Bending: A Natural Consequence of Base Sequence Dependent Variability in Biopolymer Conformations (Eds. S. Ramashesan and P. Balaram) pp 347-362.

  61. Bhattacharyya and M. Bansal) (1990) Local Variability and Base Sequence Effects in DNA Crystal Structures J. Biomol. Struct. Dynam. 8, 539-572.

  62. Bhattacharyya and M. Bansal (1989) A Self-Consistent Formulation for Analysis and Generation of Nun-Uniform DNA Structures J. Biomol. Struct. Dynam. 6, 645-653.

  63. Bansal and D. Bhattacharyya (1989) Real and Apparent Curvature in Oligonucleotides in Structure & Methods, vol. 3 (Eds. R.H. Sarma and M.H. Sarma) pp. 139-153.

  64. Bhattacharyya and M. Bansal (1988) A General Procedure for Generation of Curved DNA Molecules J. Biomol. Struct. Dynam. 6, 93-104.

  65. Bhattacharyya and M. Bansal) (1988) Why do DNA Helical Models Exhibit Wedge Rolls? A Mathematical Rationale Current Science 57, 1159-1162.

  66. Bhattacharyya and M.Bansal (1987) Energetics of Left and Right Handed Models of DNA J. Biomol. Struct. Dynam. 4, 1027-1040.




Software Publication :


1. M. Bansal and _D. Bhattacharyya_ (1990) NUPARM - A Nucleic Acid

Parameter Determination Program, /distributed by Brookhaven Protein Data

Bank (ftp://ftp.rcsb.org/pub/pdb/software/bnl_software/nuparm) as

Program entry./