CLeFAPS: Fast Flexible Alignment of Protein Structures Based on Conformational Letters

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.