Protein Structure Alignment Methods Based On AFPs

The Human Genome Project was declared complete in 2003, indicating that 90% of the genome found in human cells was sequenced. With the development of research on genetic mechanism, central dogma of molecular biology was proposed that DNA information can be copied into mRNA and proteins can be synthesized using the information in mRNA as a template. The dogma reflects that DNA plays a role in genetic mechanism by controlling proteins. Therefore, it is important for researchers to explore the relationship between protein structure and function. In biology, there is an universal principle that function is determined by structure. In order to enhance the understanding of protein function, how to find protein structure similarities is a fundamental question. In other words, finding the similarities between protein structures can help biologists explore protein functions.However, it is difficult for researchers to manually compare protein structures mainly because of the complexity of protein structure and a large number of known protein structures. Therefore, computer is used to align protein structures in bioinformatics. How to look for similarities of protein structures by computer becomes an essential problem. Although many algorithms have been proposed for protein structure alignment, such as CE,DALI,TM-align,FATCAT, these algorithms cannot achieve satisfying results in aligning protein structures and there is still room for improvement in their performance.After briefly introducing 6 kinds of protein structure alignment methods, including DALI, CE, FATCAT, TM-align, FlexProt and FlexSnap, two new methods for protein structure alignment are developed in the paper: VALAFP and FlexVAFP. These two methods both use the concept of variable-length AFP(Aligned Fragment Pairs). Different from the VALAFP method which treats proteins as rigid bodies without physical deformation, FlexVAFP considers the flexibility of protein structures. In the evaluation of their performance, these two proposed methods, VALAFP and FlexVAFP, can achieve competitive results compared to other state-of-the-art methods. Meanwhile, they improve the efficiency of the structure alignment compared with other AFP-based protein structure alignment methods, such CE and FATCAT.