All programs updated in November 2025 to use the new BiopLib library
and findcora tidied up to match our coding standards.
The original findcore program was written in 1996 as part of the
analysis of the CASP2 comparative (template-based) modelling
assessment. This was based on taking two structures fitted using
Christine Orengo's SSAP software which performed a structural
alignment and contained secondary structure assignments in its output.
The program reads the SSAP alignment and performs a fit between the
structures based on that alignment. It then throws out residue pairs
that have a C-alpha separation of >3A and grows the fitted regions
while the deviation C-alpha separation is <=3A. The fitting and zone
adjustment then iterated until no more residue pairs are added or
removed. (The default 3A cutoff can be changed on the command line.)
The final set of residues used for fitting is defined as the core.
findcora is a modification of the findcore program done by Gabby
Marsden (nee Reeves), a PhD student working with Christine Orengo and
Andre Martin. She modified the program so that it could work with
multiple structure alignments from Cora rather than pairwise
alignments from SSAP.
ProFit is Andrew Martin's protein least-squares fitting software.
After findcore was written, ProFit was enhanced to add an
iterative structural alignment feature. This uses a seed alignment
(typically the sequence alignment) as a proxy for the structural
alignment; it then fits the structures and uses a dynamic programming
algorithm to update the equivalenced residues, and at the same time
brings in residue pairs with C-alpha separation of <=3A and throwing
out those with separation >3A. This then iterates to convergence. As
with findcore, this 3A cutoff can be changed.
Consequently, ProFit is doing a combination of what SSAP and
findcore were doing.
profitcore is a new program (November 2025) that takes the
sequentially numbered zones generated by ProFit and converts them to
residue number ranges (using the residue number labels found in the
PDB files). Optionally it will write PDB files where the zones used
for fitting (i.e. the core) have a B-value of 1.0 while all other
atoms have a B-value of 0.0.
Currently profitcore only handles 2 structures (i.e. like SSAP and
findcore), but will soon be updated to handle multiple structure
(like CORA and findcora).
Compilation requires our bioplib library to be installed. It is then
just a case of typing make in the src directory.