Algorithms for detecting structure similarity ynamIc Programming works on 1D strings-reduce problem to this cant accommodate topological changes example: Secondary Structure Alignment Program(SSAP) 3D Comparison/Clustering identify secondary structure elements or fragments look for a similar arrangement of these between different structures allows for different topology, large insertions example: Vector Alignment Search Tool (VAST) Distance matrix identify contact patterns of groups that are close together compare these for different structures fast. insensitive to insertions example: Distance ALIgnment Tool(DALI) Unit vector rMs lap structure to sphere of vectors minimize the difference between spheres fast. insensitive to outliers example: Matching Molecular Models obtained from Theory (MAMMOTHAlgorithms for detecting structure similarity Dynamic Programming - works on 1D strings - reduce problem to this - can’t accommodate topological changes - example: Secondary Structure Alignment Program (SSAP) 3D Comparison/Clustering - identify secondary structure elements or fragments - look for a similar arrangement of these between different structures - allows for different topology, large insertions - example: Vector Alignment Search Tool (VAST) Distance Matrix - identify contact patterns of groups that are close together - compare these for different structures - fast, insensitive to insertions - example: Distance ALIgnment Tool (DALI) Unit vector RMS - map structure to sphere of vectors - minimize the difference between spheres - fast, insensitive to outliers - example: Matching Molecular Models Obtained from Theory (MAMMOTH)