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Structural comparison

By: Z. S. Rezaei. Structural comparison. Structural comparison. Structural alignment spectrum of structural alignment methods The properties of output Types of comparison Algorithmic complexity Representation of structures Distance matrix Methods Alignment of large RNA molecules

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Structural comparison

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  1. By: Z. S. Rezaei Structural comparison

  2. Structural comparison • Structural alignment • spectrumof structural alignment methods • The properties of output • Types of comparison • Algorithmic complexity • Representation of structures • Distance matrix • Methods • Alignment of large RNA molecules • The classes of scoring

  3. Structural alignment • homology between two or more polymer (2) • a window into the distant past of protein evolution(1) • identification homologous(1) • imply evolutionary relationships between proteins that share very little common sequence(2) • prediction of the functions and the family of the query protein(2)

  4. rely on information about conformations.( from X-ray crystallography or NMR spectroscopyor structure predictionmethods) for evaluating prediction methods Structural alignment

  5. spectrumof structural alignment methods(1)

  6. The properties of out put • a superposition of the atomic coordinatesets and a minimal RMSD. • existence of multiple protein domains complicates the Structural alignment • a set of superposed three-dimensional coordinates for each input structure(2)

  7. the root mean square(RMS) (3) Definition of RMS

  8. Definition of coordinate system(5)

  9. Coordinate system • Spatial coordinate • Planar coordinate

  10. Types of comparisons • Structuralsuperposition used to compare multiple conformations of the same protein uses a simple least-squares fitting algorithm(2) • Alignment Algorithms based on multidimensional rotations and modified quaternions (2)

  11. a number system In mathematics a quaternion as the quotient of two directed lines in a three-dimensional represented as the sum of a scalar and a vector (6) Definition of quaternion

  12. Algorithmic complexity • Optimal solution • Approximate solution(2)

  13. Optimal solution • The optimal "threading" shown to be NP-complete • Strictly speaking, an optimal solution is only known for certain protein structure similarity measures • the algorithm for optimal solution is not practical(2)

  14. Approximate solution

  15. Representation of structures

  16. distance matrix

  17. Methods(2) • DALI • Combinatorialextension(CE) • GANGSTA+ • MAMMOTH • ProBiS • RAPIDO • SABERTOOTH • SSAP • Spalign • TOPOFIT • SSM

  18. DALI • distance alignment matrix method • breaks the input structures into hexapeptide fragments and calculates a distance matrix • Distance matrix has two diagonals • conducted via a series of overlapping submatrices of size 6x6 • Submatrix matches are reassembled into a final alignment

  19. DALI • The original version used a Monte Carlo simulation • The DALI method has also been used to construct a database known as FSSP (Fold classification based on Structure-Structure alignment of Proteins, or Families of Structurally Similar Proteins) • There is an searchable database based on DALI as well as a downloadable program and web search based on a standalone version known as DaliLite.

  20. Montecarlo method

  21. http://ehkinda.biocenter.helsinki.fi/dali_server/

  22. http://ebi.ac.uk/Tools/structure/dalilite

  23. http://ebi.ac.uk/Tools/structure/dalilite

  24. http://ebi.ac.uk/Tools/structure/dalilite

  25. http://ebi.ac.uk/Tools/structure/dalilite

  26. Combinatorial extension(CE)

  27. Combinatorial extension(CE) • initial AFP pair that nucleates the alignment • proceed with the next AFP • The RCSB PDB has recently released an updated version of CE and FATCAT as part of the RCSB PDB Protein Comparison Tool • provides a new variation of CE that can detect circular permutations in protein structures

  28. Circular permutations • A circular permutation is a relationship between proteins whereby the proteins have a changed order of amino acids in their peptide sequence. The result is a protein structure with different connectivity, but overall similar three-dimensional (3D) shape(7)

  29. GANGSTA+ • A combinatorial algorithm for non-sequential structural alignment of proteins • searching for similarity in databases (http://agknapp.chemie.fu-berlin.de/gplus/) • evaluates based on contact maps and secondry structure

  30. MAMMOTH • MAtchingMolecular Models Obtained from Theory • For comparing models coming from structure prediction • decompose the protein structure into heptapeptides • The similarity score between two heptapeptides is calculated using a unit-vector RMS (URMS) method • These scores are stored in a similarity matrix • Derived from the likelihood of obtaining a given structural alignment by chance

  31. MAMMOTH-mult • extension of the MAMMOTH algorithm • is very fast • produces consistent and high quality structural alignments • produces structurally implied sequence alignments that can be further used for multiple-template homology modeling

  32. ProBiS • Protein Binding Sites. ProBiS • detects structurally similar sites on protein surfaces • compares the query protein to members of a database of protein 3D structures • Using an efficient maximum clique algorithm • Structural similarity scores are calculated for the query protein’s surface residues, and are expressed as different colors • used successfully for the detection of protein–protein, protein–small ligand and protein–DNA binding sites

  33. RAPIDO • Rapid Alignment of Proteins In terms of Domains • a web server for the 3D alignment of crystal • using an approach based on difference distance matrices • The Matching Fragment Pairs (MFPs) are then represented as nodes in a graph • nodes in graph are chained together to form an alignment by means of an algorithm for the identification of the longest path on a DAG (Directed Acyclic Graph). • The final step: improve the quality of the alignment

  34. SABERTOOTH • structural profiles to perform structural alignments • has favourable scaling of computation time with chain length • SABERTOOTH can be used online at http://www.fkp.tu-darmstadt.de/sabertooth/

  35. SSAP • Sequential Structure Alignment Program • uses double dynamic programming • constructs its vectors from the beta carbons for all residues except glycine • A series of matrices are constructed • Dynamic programming applied to each resulting matrix • matrices are then summed into a "summary" matrix to • Final dynamic programming is applied again to determine the overall structural alignment

  36. SSAP • originally produced only pairwise alignments • but has since been extended to multiple alignments as well • applied in an all-to-all fashion to produce a hierarchical fold classification scheme known as CATH (Class, Architecture, Topology, Homology) • construct the CATH Protein Structure Classification database

  37. SPalign • Based on a new size-independent score called SPscore for • The source code for SPalign and the server are available at http://sparks.informatics.iupui.edu/yueyang/server/SPalign/

  38. TOPOFIT • Based on Delaunay tessellation (DT) • identifies a feature point on the RMSD/Ne curve • topomax point • to detect conformational changes, topological differences in variable parts

  39. SSM • Secondary Structure Matching (SSM), or PDBeFold at the Protein Data Bank in Europe • uses graph matching followed by c-alpha alignment to compute alignments

  40. Recent Developments

  41. RNA structural alignment • large RNA molecules also form characteristic tertiary structures • A recent method for pairwise structural alignment of RNA sequences implemented in the program FOLDALIGN • In low sequence identity cases

  42. (1)

  43. References • Hitomi Hasegawa and Liisa Holm: Advances and pitfalls of protein structural alignment, Current Opinion in Structural Biology 2009, 19:341–348 • en.wikipedia.org/wiki/structural_alignment software • Cartwright, Kenneth V (Fall 2007). "Determining the Effective or RMS Voltage of Various Waveforms without Calculus". Technology Interface8 (1): 20 pages • Anderson, H.L. (1986). "Metropolis, Monte Carlo and the MANIAC". Los Alamos Science14: 96–108 • Weisstein, Eric W., "Coordinate System" from MathWorld • Boris AbramovichRozenfelʹd (1988). The history of non-euclidean geometry: evolution of the concept of a geometric space. Springer. p. 385 • Cunningham, B. A.; Hemperly, J. J.; Hopp, T. P.; Edelman, G. M. (1979). "Favin versus concanavalin A: Circularly permuted amino acid sequences". Proceedings of the National Academy of Sciences of the United States of America76 (7): 3218–3222

  44. I am ready to answer your questions

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