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BPFIND & NUPARM Server

An expert that computes everything of RNA

Introduction

BPFind is a software tool for detecting stable and feasible basepairs present in nucleic acid molecules. It finds potential H-bonds within the molecule and checks for the basepair geometry to output the best possible pairing pattern between a pair of bases. BPFind considers both the standard N/O-H...N/O and non-polar C-H...O/N types of hydrogen bonding. However, one can also detect those basepairs stabilized only by regular polar hydrogen bonds. BPFind considers two bases as paired only when it finds at least two hydrogen bonds between the bases.


Input File Type
  1. Files containing coordinates of the atoms in PDB format (XXXX.pdb)
  2. Files containing coordinates of the atoms in mmCIF format (XXXX.cif)
  3. Files containing coordinates of atoms obtained from NMR or MD simulation, with many models in the same file.