NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. - Manju Bansal; Dhananjay Bhattacharyya; B. Ravi (Comput. Appl. Biosci., 1995)

NUVIEW: software for display and interactive manipulation of nucleic acid models. - Manju Bansal; Dhananjay Bhattacharyya; S. Vijaylakshmi (Comput. Appl. Biosci., 1995)

Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. - Shayantani Mukherjee; Manju Bansal; Dhananjay Bhattacharyya (J. Comput. Aided Mol. Des., 2006)

Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs. - Sankar Basu; Dhananjay Bhattacharyya; Rahul Banerjee (BMC Bioinform., 2011)

Modeling the Closed and Open State Conformations of the GABAA Ion Channel - Plausible Structural Insights for Channel Gating. - R. S. K. Vijayan; Neha Trivedi; Sudipendra Nath Roy; Indrani Bera; Prabu Manoharan; Pavan V. Payghan; Dhananjay Bhattacharyya; Nanda Ghoshal (J. Chem. Inf. Model., 2012)

Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs. - Sanchita Mukherjee; Sangeeta Kundu; Dhananjay Bhattacharyya (J. Comput. Aided Mol. Des., 2014)

Analysis of stacking overlap in nucleic acid structures: algorithm and application. - Pavan Kumar Pingali; Sukanya Halder; Debasish Mukherjee; Sankar Basu; Rahul Banerjee; Devapriya Choudhury; Dhananjay Bhattacharyya (J. Comput. Aided Mol. Des., 2014)

RNABP COGEST: a resource for investigating functional RNAs. - Sohini Bhattacharya; Shriyaa Mittal; Swati Panigrahi; Purshotam Sharma; Preethi S. P.; Rahul Paul; Sukanya Halder; Antarip Halder; Dhananjay Bhattacharyya; Abhijit Mitra (Database J. Biol. Databases Curation, 2015)

Role of indirect readout mechanism in TATA box binding protein-DNA interaction. - Manas Mondal; Devapriya Choudhury; Jaydeb Chakrabarti; Dhananjay Bhattacharyya (J. Comput. Aided Mol. Des., 2015)

RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs. - Dhananjay Bhattacharyya; Sukanya Halder; Sankar Basu; Debasish Mukherjee; Prasun Kumar; Manju Bansal (J. Comput. Aided Mol. Des., 2017)

Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches. - Lakshmi Maganti; Dhananjay Bhattacharyya (J. Comput. Aided Mol. Des., 2020)

MetBP: a software tool for detection of interaction between metal ion-RNA base pairs. - Parthajit Roy; Dhananjay Bhattacharyya (Bioinform., 2022)

Contact networks in RNA: a structural bioinformatics study with a new tool. - Parthajit Roy; Dhananjay Bhattacharyya (J. Comput. Aided Mol. Des., 2022)

Microscopic model on indoor propagation of respiratory droplets. - Manas Mondal; Srabani Chakrabarty; Yi Qin Gao; Dhananjay Bhattacharyya; Jaydeb Chakrabarti (Comput. Biol. Chem., 2023)