How to fix missing (superfluous) base pairs identified by find_pair?
Structural analysis of nucleic acid used to be a rather tedious process, especially for irregular, complicated RNA structures and nucleic acid – protein complexes (e.g., the large ribosomal subunit 1jj2/RR0033). Without valid base-pairing information as input, the various analysis software will produce meaningless results. The program find_pair was originally created to solve this specific problem, by generating input file to 3DNA analysis routines directly from a PDB file. In its core, find_pair uses a pure geometric approach to identify all possible pairs (canonical A-T and C-G, or whatever pairs that actually exist in a structure), their H-bonding patterns and helix context.
