Structural Biochemistry/Bioinformatics/Structural Alignments/Programs Used For Structural Alignment/RAPIDO
RAPIDO stands for Rapid Alignment of Proteins in terms of DOmains. RAPIDO is a web sever for 3D alignment of crystal structures of different protein molecules in the presence of conformational changes. Similar to CE's first step, RAPIDO identifies fragments that are structurally similar in two different proteins using an approach that uses difference distance matrices. The MFPs (Matching Fragments Pairs) are represented as nodes in a graph which are chained together to form an alignment by means of an algorithm for identification of the longest path on a DAG (Directed Acyclic Graph). The last step of refinement is performed to improve quality of the performed alignment. After aligning the two structures, the server applies a genetic algorithm for identification of conformationally invariant regions. These regions correspond to groups of atoms with constant inter atomic distances (within a defined tolerance). By doing this, RAPIDO takes into account variation in the reliability of atomic coordinates by employing weighting-functions based on the refined B-values. The regions that are identified as conformationally invariant by RAPIDO represent reliable sets of atoms for the superposition of the two structures that can be used for detailed analysis of changes in the conformation. RAPIDO can identify structurally equivalent regions even when these consist of fragments that are distant in terms of sequence and separated by other movable domains.