The server would identify base pairs from the chosen file by using BPFIND software (1). This hypothesis driven algorithm looks for at least two hydrogen bonds between the bases.
The Intra base pair and Inter base pair parameters along with several other parameters would be calculated using base pairing edge specific axis system using NUPARM (2, 3, 4).
1. Non-Canonical Base Pairs and Higher Order Structures in Nucleic Acids: Crystal Structure Database Analysis. J. Das, S. Mukherjee, A. Mitra, D. Bhattacharyya (2006) J. Biomol. Struct. Dynam. 24: 149-161.
2. NUPARM and NUCGEN: Software for Analysis and Generation of Sequence Dependent Nucleic Acid Structures. M. Bansal, D. Bhattacharyya, B. Ravi. (1995) CABIOS 11: 281-287.
3. Conformational Specificity of Non-canonical Base Pairs and Higher Order Structures in Nucleic Acids: Crystal Structure Database Analysis. S. Mukherjee, M. Bansal, D. Bhattacharyya (2006) J. Comp. Aided Mol. Des. 20: 629-645.
4. Analysis of stacking overlap in nucleic acid structures: algorithm and application. P. K. Pingali, S. Halder, D. Mukherjee, S. Basu, R. Banerjee, D. Choudhury,D. Bhattacharyya (2014) J. Comp. Aided Mol. Des. 28: 851-867.
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