The structure of a protein is dictated by a large number of weak interactio
ns that cooperatively stabilize the native state. Usually, excised fragment
s smaller than a domain have Little if any residual structure. When autonom
ous units of structure are found within domains, this challenges common ass
umptions about the cooperativity of protein structure. Such autonomous fold
ing units (AFUs) are of wide interest and have applications in protein engi
neering and as simple model systems for studying the determinants of stabil
ity and specificity. A new method of identifying AFUs within proteins is pr
esented here. The rapid autonomous fragment test (RAFT) identifies AFUs bas
ed on analysis of inter-residue contacts present in the three-dimensional s
tructure of a protein. RAFT is fast enough to mine the entire PDB for AFUs
and provide a library of potential small stable folds. We show that RAFT is
able to predict whether a protein fragment will be structured if isolated
from its parent domain. (C) 2000 Academic Press.