1. Lab Meeting 06/05/20051 NMRQ: Quality Assessment and Validation for Protein Structures Generated by NMR Spectroscopy Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca May 06, 2005

2. Lab Meeting 06/05/20052 Introduction Protein structure determination is important for: –Protein functional characterization –Rational drug design –Biological understanding Protein structures must be reliable and accurate to be useful. Protein structures can be determined by X-ray crystallography and by NMR spectroscopy

3. Lab Meeting 06/05/20053 Introduction Protein structure generation by either method is prone to experimental and interpretation error. Protein structure analysis programs are available to assess protein structure quality: –WHATCHECK –PROCHECK & PROCHECK-NMR –PROVE –SQUID –VADAR –MOLPROBITY –Coming Soon: NMRQ!

4. Lab Meeting 06/05/20054 Introduction Protein Structure Validation Packages: –Verify the structure file syntax –Check the consistency of the structure against a library of high-quality structures and identify outliers –Detect gross errors in the model –Check for local stereochemical abnormalities –Produce a score to describe the quality of the structure

5. Lab Meeting 06/05/20055 WHAT CHECK Stereochemical Analysis Postscript/Text/HTML “Z” Scores Crude Graphics Does not perform “ensemble analysis”

6. Lab Meeting 06/05/20056 PROCHECK-NMR Sterochemical Analysis Restraint Analysis via AQUA Ensemble Analysis Postscript Good Graphics Times Cited: 6390

7. Lab Meeting 06/05/20057 NMRQ Sterochemical Analysis Restraint Analysis Ensemble Analysis Chemical Shift Analysis Superposition and RMSD HTML Reports

8. Lab Meeting 06/05/20058 NMRQ

9. Lab Meeting 06/05/20059 NMRQ

10. Lab Meeting 06/05/200510 NMRQ: Superposition

11. Lab Meeting 06/05/200511 NMRQ: Superposition

12. Lab Meeting 06/05/200512 NMRQ: Superposition

13. Lab Meeting 06/05/200513 Torsion Angle Analysis

14. Lab Meeting 06/05/200514 Torsion Angle Analysis

15. Lab Meeting 06/05/200515 Torsion Angle Analysis

16. Lab Meeting 06/05/200516 Torsion Angle Analysis

17. Lab Meeting 06/05/200517 Torsion Angle Analysis Favorable Allowed Generously Allowed Disallowed

18. Lab Meeting 06/05/200518 Torsion Angle Analysis

19. Lab Meeting 06/05/200519 Torsion Angle Analysis

20. Lab Meeting 06/05/200520 Torsion Angle Analysis

21. Lab Meeting 06/05/200521 Chi Angle Analysis

22. Lab Meeting 06/05/200522 Relation Between  and 

23. Lab Meeting 06/05/200523 SCWRL The SCWRL rotamer library is a backbone dependant rotamer library aa phi psi prob. chi1 chi2 chi3 chi4 sd1 sd2 sd3 sd4 ARG -180 -180 6 1 1 1 1 0.002977 55.4 79.7 62.4 82.3 19.8 16.1 15.0 11.9 ARG -180 -180 6 1 1 1 2 0.006091 59.2 85.4 68.2 -166.5 23.2 16.6 15.4 25.6 ARG -180 -60 0 1 3 3 1 0.000078 63.6 -77.9 -77.1 102.9 23.8 19.7 21.6 14.2

24. Lab Meeting 06/05/200524 NMRQ: Chi Angle Analysis Adds the probability values for all chi angle distributions within +/- 20 degrees, for a given phi, psi. #Sequence Chi1 Probability Secondary Structure Y-1 -64.90 0.00000 C K-2 -73.10 0.43090 C C-3 166.20 0.00000 C G-4 0.00 0.00000 C L-5 -54.90 0.60453 C

25. Lab Meeting 06/05/200525 Aside: Parsing the SCWRL Library -rw-rw-r-- 1 gvd gvd 4.0K Dec 13 16:57 RotamerLibrary.index.dir -rw-rw-r-- 1 gvd gvd 2.0M Dec 13 16:57 RotamerLibrary.index.pag -rw-r--r-- 1 gvd gvd 48M Dec 13 11:28 RotamerLibrary.txt unless ($self->{_ROTAMER_LIBRARY}{"$res $phi $psi"}) { tie (%rotLib, 'SDBM_File', $dbPath, O_RDONLY,0666) || throw Error::Simple("CreateRotamerLibrary: Could not create the DB: $!"); my $key = "$res $phi $psi"; my $val = $rotLib{$key}; # get the info from file. my ($start,$offset) = split(/\,/,$val); seek(LIBRARY, $start,0); my $buffer; read(LIBRARY,$buffer,$offset);... push @{$self->{_ROTAMER_LIBRARY}{"$res $phi $psi"}}, \%row; }

26. Lab Meeting 06/05/200526 Chi-Angle Dispersion Correlates With Accessible Surface Area Fractional ASA

27. Lab Meeting 06/05/200527 Chi Angle Analysis

28. Lab Meeting 06/05/200528 Chi Angle Analysis

29. Lab Meeting 06/05/200529 Volume and Area Loose Packing Dense Packing Protein Proteins are Densely Packed

30. Lab Meeting 06/05/200530 Volume and Area

31. Lab Meeting 06/05/200531 Volume and Area

32. Lab Meeting 06/05/200532 Volume and Area

33. Lab Meeting 06/05/200533 Volume and Area

34. Lab Meeting 06/05/200534 Volume and Area Solvent Probe Accessible Surface Van der Waals Surface Reentrant Surface

35. Lab Meeting 06/05/200535 Volume and Area

36. Lab Meeting 06/05/200536 Chemical Shift Analysis

37. Lab Meeting 06/05/200537 Chemical Shift Analysis

38. Lab Meeting 06/05/200538 Chemical Shift Analysis

39. Lab Meeting 06/05/200539 Chemical Shift Analysis

40. Lab Meeting 06/05/200540 Chemical Shift Analysis

41. Lab Meeting 06/05/200541 Other Statistics

42. Lab Meeting 06/05/200542 Other Statistics

43. Lab Meeting 06/05/200543 Other Statistics

44. Lab Meeting 06/05/200544 Other Statistics

45. Lab Meeting 06/05/200545 Other Statistics

46. Lab Meeting 06/05/200546 Summary Reports

47. Lab Meeting 06/05/200547 Summary Reports

48. Lab Meeting 06/05/200548 Summary Reports

49. Lab Meeting 06/05/200549 Restraint Analysis

50. Lab Meeting 06/05/200550 Restraint Analysis Coming Soon... PROCHECK-NMR + AQUA: –Distance restraints plot –Restraint differences plot –Numbers of distance restraints –Actual distance - restraint summary –Violation frequency summary –Restraint statistics –Residue-by-residue restraint violations –Model-by-model violations

51. Lab Meeting 06/05/200551 NMRQ TODO List Chi angle plots, and cumulative plots Restraint analysis Model and ensemble scoring statistics Syntax Validation

52. Lab Meeting 06/05/200552 NMRQ Limitations NO Chi1-Chi2 Torsion Angle Distribution PDB parsing not robust, no validation Hydrogen bond analysis available, not implemented. Insert your comments here.

53. Lab Meeting 06/05/200553 Acknowledgements Dr. Paul Stothard Trent Bjorndahl Steve Neal Prof. David Wishart