bpfind server




bpfind is the server that gives the basepairing information of pdb files.



pdbid: Insert pdbid like 1GTR/1gtr

Change the parameters below if you do not wish to run default setup [Default]ErrorInfoJeffrey[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: [default : 3.8] This is just an example
pseudo angle cutoff: [default : 120] This is just an example
E-value cutoff: [default : 1.8] This is just an example
select desired chain identifier in PDB File: [default : all] This is just an example
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