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BPFIND Server



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Click here to change the default parameters set for BPFIND run [Default]InfoJeffrey[2] categorizes H bonds with donor-acceptor distances of 2.2-2.5 Å as “strong, mostly covalent”,
2.5-3.2 Å as “moderate, mostly electrostatic”,
3.2-4.0 Å as “weak, electrostatic”
hydrogen bond distance cutoff:
pseudo angle cutoff:
E-value cutoff:
select desired chain identifier in PDB File:
Structure solved using NMR
include HETATM entries in PDB
avoid identification of base pairs stabilized by C-H...O/N H-bonds
avoid identification of base pairs involvingsugar 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

This server identifies all base pairs in a DNA or RNA structure either obtained from pdb or uploaded as file.cif in mmCif format. The algorithm for identification of base pairs depends on ability of the two bases to form AT LEAST TWO HYDROGEN BONDS between the bases or involving 2'-OH group of ribose sugar of one of the base. The method was described in Das et al. 2006 J Biomol Struct Dyn. 2006; 24: 149-61. Considering these base pair can form double helical structures in RNA it also gives positions of those helical structures.


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