Flexible protein structure alignment by variable-length Aligned Fragment Pairs

With the growing number of known protein 3D structures, how to efficiently compare protein structures becomes an important and challenging problem in computational structural biology. So, many protein structure alignment methods have been developed in recent years. Flexible structure alignment methods are shown to be superior to rigid structure alignment methods in identifying the structure similarities between proteins which have gone through conformational changes. It is also found that the methods based on Aligned Fragment Pairs (AFP) own special advantages in balancing global structure similarities and local structure similarities. In this work, we propose a new flexible protein 3D structure alignment method based on variable-length AFPs. Different from other methods, our method owns three special features: firstly, it uses a new AFP identification algorithm based on a local coordinate system; secondly, it allows different AFPs separated by other AFPs to share the same transformation during the concatenation; thirdly, it allows different AFPs to have different lengths, which can not only reduce the total number of AFPs, and also can improve the representation of the local structure similarities. The experiments show that, compared to three other flexible structure alignment methods, FlexProt, FATCAT and FlexSnap, the proposed method can achieve similar or better results by introducing fewer twists and in much less running time due to the reduced number of AFPs.