FastAlignmentofProteinStructuresBasedonConformationalLetters.pptVIP

Fast Alignment of Protein Structures Based onConformational Letters Wei-Mou Zheng Institute of Theoretical Physics Academia Sinica * Introduction Conformational alphabet and CLESUM CLePAPS: Pairwise structure alignment BloMAPS: Multiple structure alignment Conclusion Introduction Protein structures comparison: an extremely important problem in structural and evolutional biology. detection of local or global structural similarity prediction of the new proteins function. structures are better conserved → remote homology detection Structural comparison → organizing and classifying structures discovering structure patterns discovering correlation between structures sequences → structure prediction Conformational alphabet and CLESUM The main difference of CLePAPS from other existing algorithms for structure alignment is the use of conformational letters. Conformational letters = discretized states of 3D segmental conformations. A letter = a cluster of combinations of three angles formed by Ca pseudobonds of four contiguous residues. (obtained by clustering according to the probability distribution.) Centers of 17 conformational letters Similarity between conformational letters CLESUM: Conformational LEtter SUbstitution Matrix Mij = 20* log 2 (Pij/PiPj) ~ BLOSUM83, H ~ 1.05 constructed using FSSP representatives. typical helix typical sheet evolutionary + geometric CLePAPS: Pairwise structure alignment Structure alignment --- a self-consistent problem Correspondence Rigid transformation However, when aligning two protein structures, at the beginning we know neither the transformation nor the correspondence. DALI, CE VAST STRUCTAL, ProSup CLePAPS: Conformational Letters based Pairwise Alignment of Protein Structures Initialization + iteration Similar Fragment Pairs (SFPs); Anchor-based;