1. mandatory to put some order in such a vast wealth of structural knowledge 1 4. Nucleic acids and proteins in one and more dimensions - second part

2. Taxonomy (from Ancient Greek: τάξις taxis, "arrangement," and -νομία -nomia, "method") is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Organisms are grouped together into taxa (singular: taxon) and given a taxonomic rank; groups of a given rank can be aggregated to form a super group of higher rank and thus create a taxonomic hierarchy. 2 4. Nucleic acids and proteins in one and more dimensions - second part Learning from Biology

3. 4. Nucleic acids and proteins in one and more dimensions - second part 3 Learning from Biology

4. 4. Nucleic acids and proteins in one and more dimensions - second part 4 protein structure taxonomy

5. 5 4. Nucleic acids and proteins in one and more dimensions - second part protein structure taxonomy

6. 6 4. Nucleic acids and proteins in one and more dimensions - second part protein structure taxonomy

7. 7 4. Nucleic acids and proteins in one and more dimensions - second part protein structure taxonomy

8. 8 4. Nucleic acids and proteins in one and more dimensions - second part protein structure taxonomy

9. 9 4. Nucleic acids and proteins in one and more dimensions - second part protein structure taxonomy

10. 10 4. Nucleic acids and proteins in one and more dimensions - second part protein structure taxonomy

11. red: mainly α green: mainly β yellow: αβ blue: low content of secondary structures 11 4. Nucleic acids and proteins in one and more dimensions - second part protein structure taxonomy

12. 12 4. Nucleic acids and proteins in one and more dimensions - second part protein structure taxonomy from http://www.proteinstructures.com/Structure/Structure/protein-fold.html most of different protein folds have been already found?

13. 4. Nucleic acids and proteins in one and more dimensions - second part 13 comparing protein structure

14. 4. Nucleic acids and proteins in one and more dimensions - second part 14 comparing protein structure

15. 4. Nucleic acids and proteins in one and more dimensions - second part 15 comparing protein structure

16. 4. Nucleic acids and proteins in one and more dimensions - second part 16 1898 proteins representative of the most common fold

17. 4. Nucleic acids and proteins in one and more dimensions - second part 17

18. Structural genomics 0101#01001010#10111010# 01010001#10010#1001#101 10010#100100100101011#0 DNA Algorithm Residue  THR0.0147.7172.9 THR107.2-125.3187.4 CYS123.463.6103.7 PRO60.383.9-116.7 Protein Structure X Ray diffractometry NMR cryo-electron tomography 18 3. genome analysis

19. 4. Nucleic acids and proteins in one and more dimensions - second part 19 from structural knowledge to structural predictions

20. secondary structure prediction 20 4. Nucleic acids and proteins in one and more dimensions - second part

21. secondary structure prediction 21 4. Nucleic acids and proteins in one and more dimensions - second part

22. CHOU & FASMAN Chou, P.Y. & Fasman, G.D. (1974). Biochemistry, 13, 211-222. secondary structure prediction 22 4. Nucleic acids and proteins in one and more dimensions - second part

23. secondary structure prediction # residues in window: 6 23 4. Nucleic acids and proteins in one and more dimensions - second part

24. secondary structure prediction 24 4. Nucleic acids and proteins in one and more dimensions - second part

25. secondary structure prediction 25 4. Nucleic acids and proteins in one and more dimensions - second part

26. secondary structure prediction 26 4. Nucleic acids and proteins in one and more dimensions - second part

27. secondary structure prediction 27 4. Nucleic acids and proteins in one and more dimensions - second part

28. secondary structure prediction PSIPRED is a simple and reliable secondary structure prediction method, incorporating two feed- forward neural networks which perform an analysis on output obtained from PSI-BLAST (Position Specific Iterated - BLAST). 28 4. Nucleic acids and proteins in one and more dimensions - second part

29. secondary structure prediction 29 4. Nucleic acids and proteins in one and more dimensions - second part

30. secondary structure prediction 30 4. Nucleic acids and proteins in one and more dimensions - second part

31. 31 4. Nucleic acids and proteins in one and more dimensions - second part

32. Sequence Alignment “Two homologous sequences whisper... a full multiple alignment shouts out loud.” in Hubbard TJ, Lesk AM, Tramontano A. Gathering them in to the fold. Nat Struct Biol. 1996 Apr;3(4):313.) 32 4. Nucleic acids and proteins in one and more dimensions - second part

33. 33 4. Nucleic acids and proteins in one and more dimensions - second part

34. 34 4. Nucleic acids and proteins in one and more dimensions - second part

35. Letters corresponding to isolated matches are shown in non-bold type. The longest matching regions, shown in boldface, are the first and last names DOROTHY and HODGKIN. Shorter matching regions, such as the OTH of dorOTHy and crowfoOTHodgkin, or the RO of doROthy and cROwfoot, are noise. Dotplot showing identities between the palindromic sequence MAX I STAY AWAY AT SIX AM and itself. The palindrome reveals itself as a stretch of matches perpendicular to the main diagonal. Dotplot showing identities between a repetitive sequence (ABRACADABRACADABRA) and itself. The repeats appear on several subsidiary diagonals parallel to the main diagonal. From Introduction to Bioinformatics by Arthur M. Lesk dotplot The dotplot is a simple picture that gives an overview of the similarities between two sequences. Less obvious is its close relationship to alignments. The dotplot is a table or matrix. The rows correspond to the residues of one sequence and the columns to the residues of the other sequence. In its simplest form, the positions in the dotplot are left blank if the residues are different, and filled if they match. Stretches of similar residues show up as diagonals in the upper left-lower right (Northwest-Southeast) direction. 35 4. Nucleic acids and proteins in one and more dimensions - second part

36. 36 4. Nucleic acids and proteins in one and more dimensions - second part

37. 37 4. Nucleic acids and proteins in one and more dimensions - second part

38. BLOSUM62 matrix does an excellent job detecting similarities in distant sequences, and this is the matrix used by default in most recent alignment applications such as BLAST 38 4. Nucleic acids and proteins in one and more dimensions - second part

39. Mutation probability matrix for the evolutionary distance of 250 PAMs 39 4. Nucleic acids and proteins in one and more dimensions - second part

40. 40 4. Nucleic acids and proteins in one and more dimensions - second part

41. 41 4. Nucleic acids and proteins in one and more dimensions - second part

42. tertiary structure prediction 42 4. Nucleic acids and proteins in one and more dimensions - second part

43. tertiary structure prediction 43 4. Nucleic acids and proteins in one and more dimensions - second part

44. tertiary structure prediction 44 4. Nucleic acids and proteins in one and more dimensions - second part

45. teminates with > Amino Acid Code Meaning A Alanine B Aspartic acidAspartic acid or AsparagineAsparagine C Cysteine D Aspartic acid E Glutamic acid F Phenylalanine G Glycine H Histidine I Isoleucine K Lysine L Leucine M Methionine N Asparagine O Pyrrolysine P Proline Q Glutamine R Arginine S Serine T Threonine U Selenocysteine V Valine W Tryptophan Y Tyrosine Z Glutamic acidGlutamic acid or GlutamineGlutamine X any * translation stop - gap of indeterminate length 45 4. Nucleic acids and proteins in one and more dimensions - second part

46. 46 4. Nucleic acids and proteins in one and more dimensions - second part

47. 47 4. Nucleic acids and proteins in one and more dimensions - second part

48. tertiary structure prediction 48 4. Nucleic acids and proteins in one and more dimensions - second part

49. tertiary structure prediction 49 4. Nucleic acids and proteins in one and more dimensions - second part

50. tertiary structure prediction 50 4. Nucleic acids and proteins in one and more dimensions - second part

51. Protein folding ab initio calculations of protein structure 51 4. Nucleic acids and proteins in one and more dimensions - second part

52. MSSPQAPEDGQGCGDRGDPPGDLRSVLVTTV ROSETTA Frammenti di 9 aa Sceglie le strutture delle 25 sequenze più vicine Ottimizzazione e Assemblaggio (Knowledge-based potential) Metodo Assemblaggio di frammenti: Dividendo la sequenza in frammenti 52 4. Nucleic acids and proteins in one and more dimensions - second part

53. Rosetta Fragment Libraries 25-200 fragments for each 3 and 9 residue sequence window Selected from database of known structures > 2.5Å resolution < 50% sequence identity Ranked by sequence similarity and similarity of predicted and known secondary structure 53 4. Nucleic acids and proteins in one and more dimensions - second part

54. 54 4. Nucleic acids and proteins in one and more dimensions - second part

55. 55 RNA structure prediction

56. 4. Nucleic acids and proteins in one and more dimensions - second part 56 RNA structure prediction Secondary structure of a telomerase RNA Primary structure of RNA Tertiary structure of RNA

57. 4. Nucleic acids and proteins in one and more dimensions - second part 57 RNA structure prediction