  CLeFAPS, a fast and flexible pairwise structural alignment algorithm based on
a rigid-body framework, namely CLePAPS, is proposed. Instead of allowing twists
(or bends), the flexible in CLeFAPS means: (a) flexibilization of the
algorithm's parameters through self-adapting with the input structures' size,
(b) flexibilization of adding the aligned fragment pairs (AFPs) into an
one-to-multi correspondence set instead of checking their position conflict,
(c) flexible fragment may be found through an elongation procedure rooted in a
vector-based score instead of a distance-based score. We perform a comparison
between CLeFAPS and other popular algorithms including rigid-body and flexible
on a closely-related protein benchmark (HOMSTRAD) and a distantly-related
protein benchmark (SABmark) while the latter is also for the discrimination
test, the result shows that CLeFAPS is competitive with or even outperforms
other algorithms while the running time is only 1/150 to 1/50 of them.
