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BPFIND & NUPARM Server

An expert that computes everything of RNA

About BPFIND and NUPARM

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).

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Change The Default for BPFIND  
Jeffrey[2] categorizes H bonds with donor-acceptor distances of 2.2-2.5 angstorm as "strong, mostly covalent", 2.5-3.2 Angstorm as "moderate, mostly electrostatic", 3.2-4.0 Angstorm as "weak, electrostatic".
Hydrogen bond distance cutoff:
Pseudo angle cutoff:
E-value cutoff:
Select desired chain identifier in PDB entry:
Select desired NMR model in the File:
Include HETATM entries in PDB
Avoid identification of base pairs stabilized by C-H...O/N H-bonds
Avoid identification of base pairs involving sugar O2' atoms
Avoid base pairing between residue no. i and i+1
Avoid printing base pairing information w.r.t. the second strand.
This is suitable for simple oligonucleotides

Change The Default for NUPARM
Jeffrey[2] categorizes H bonds with donor-acceptor distances of 2.2-2.5 angstorm as "strong, mostly covalent", 2.5-3.2 Angstorm as "moderate, mostly electrostatic", 3.2-4.0 Angstorm as "weak, electrostatic".
Do not use default cross-product method:
Use C1' - C1' as Y-axis:
Do not use C6-C8 midpoint as BP center
Required Single stranded parameters:
                       Consider all base pairs as Watson-Crick type:               





References:
  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.

  5. External Programs:VARNA: Interactive drawing and editing of the RNA secondary structure. Kévin Darty, Alain Denise and Yann Ponty. Bioinformatics, pp. 1974-1975, Vol. 25, no. 15, 2009.