Structural alignment and comparison are important tools in the study of protein structure and function. These methods allow for the identification of similarities and differences between protein structures, which can provide insight into their evolutionary relationships and functional properties. Here are some commonly used structural alignment and comparison algorithms:
- DALI: DALI (Distance-matrix ALIgnment) is a structural alignment algorithm that compares the 3D structures of two proteins based on their overall shape and spatial arrangement of secondary structure elements. DALI generates a structural alignment score (Z-score) that reflects the degree of similarity between the two structures.
- TM-align: TM-align is a structural alignment algorithm that measures the similarity between two protein structures based on their overall shape and spatial arrangement of alpha-helices and beta-sheets. TM-align generates a structural alignment score (TM-score) that reflects the degree of similarity between the two structures.
- CE: CE (Combinatorial Extension) is a structural alignment algorithm that compares the 3D structures of two proteins based on their overall shape and spatial arrangement of backbone atoms. CE generates a structural alignment score that reflects the degree of similarity between the two structures.
- SSM: SSM (Secondary Structure Matching) is a structural alignment algorithm that compares the 3D structures of two proteins based on the spatial arrangement of secondary structure elements. SSM generates a structural alignment score that reflects the degree of similarity between the two structures.
- FATCAT: FATCAT (Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists) is a flexible structural alignment algorithm that compares the 3D structures of two proteins based on the spatial arrangement of aligned fragment pairs. FATCAT generates a structural alignment score that reflects the degree of similarity between the two structures.
Overall, the choice of structural alignment and comparison algorithm depends on the specific research question and the nature of the protein structures being compared. Each algorithm has its own strengths and weaknesses and may be more suitable for certain types of proteins or structural features.