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

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

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

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

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

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

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

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

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

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

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

12. protein structure taxonomy
most of different protein folds have been already found?
from
4. Nucleic acids and proteins in one and more dimensions - second part

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

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

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

16. Structural genomics NMR DNA Protein Structure Algorithm
X Ray diffractometry
NMR
Residue   
THR
0.0
147.7
172.9
107.2
-125.3
187.4
CYS
123.4
63.6
103.7
PRO
60.3
83.9
-116.7
Protein Structure
cryo-electron tomography
DNA
0101# # #
#10010#1001#101
10010# #0
Algorithm
3. genome analysis

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

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

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

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

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

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

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

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

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

26. 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).
4. Nucleic acids and proteins in one and more dimensions - second part

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

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

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

30. 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 Apr;3(4):313.)
4. Nucleic acids and proteins in one and more dimensions - second part

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

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

33. 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.
Dotplot showing identities between a repetitive sequence (ABRACADABRACADABRA) and itself. The repeats appear on several subsidiary diagonals parallel to the main diagonal.
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.
From Introduction to Bioinformatics
by Arthur M. Lesk
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35. 4. Nucleic acids and proteins in one and more dimensions - second part

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

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

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

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

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

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

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

43. 4. Nucleic acids and proteins in one and more dimensions - second part
Amino Acid Code
Meaning A
Alanine B
Aspartic acid or Asparagine 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 acid or Glutamine X
any *
translation stop -
gap of indeterminate length
teminates with >
4. Nucleic acids and proteins in one and more dimensions - second part

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

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

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

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

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

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

51. Rosetta Fragment Libraries
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
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52. 4. Nucleic acids and proteins in one and more dimensions - second part

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

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

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