Download

Homology Modeling






Advertisement
Download Presentation
Comments
albert
From:
|  
(4914) |   (0) |   (0)
Views: 242 | Added: 24-11-2011
Rate Presentation: 0 0
Description:
Part 1 Monday 1:30-3:00pm. . Homology Modeling - I (Comparative Modeling). What is it and why do we need it?principles of modeling, applications availableUsing Swiss-Modelpreparation, workspace tools, automated-moderefining with manually-adjusted alignmentsModel Assessmentusing Swiss-Model tools to check model qualitywhat to look for, what we expect
Homology Modeling

An Image/Link below is provided (as is) to

Download Policy: Content on the Website is provided to you AS IS for your information and personal use only and may not be sold or licensed nor shared on other sites. SlideServe reserves the right to change this policy at anytime. While downloading, If for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.











- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -




1. Homology Modeling Masa Watanabe University of California - Merced

3. Homology Modeling - I (Comparative Modeling) What is it and why do we need it? principles of modeling, applications available Using Swiss-Model preparation, workspace tools, automated-mode refining with manually-adjusted alignments Model Assessment using Swiss-Model tools to check model quality what to look for, what we expect?

4. Why is Homology Modeling? Given an unknown protein, make an informed guess on its 3D structure based on its sequence: Search structure databases for homologous sequences Transfer coordinates of known protein onto unknown

5. Why Modeling is Necessary Current structure determination methods: NMR ? conc. protein solution; limited size + resolution XRay Crystallography ? protein crystals, high resolution Expensive, slow, difficult (especially membrane proteins!) Can?t keep up with growth rate of sequence databases: PDB: 56800 Protein structures (as of 11/10/2009 ) http://www.pdb.org/ UniProt Knowledgebase: 512000+ sequences (as of 11/03/2009 ) http://au.expasy.org/sprot/

6. High Expectation in Modeling? At the very best, however, you cannot learn fine details of side-chain conformations, as you can from determining protein structure by X-ray crystallography or NMR. But homology models can be useful for preliminary exploration, and might also point to useful target residues for chemical analyses of structure, such as site-directed mutagenesis.

7. SWISS-MODEL (www) http://swissmodel.expasy.org/ 3D-Jigsaw (www) http://www.bmm.icnet.uk/servers/3djigsaw/ ESyPred3D (www) http://www.fundp.ac.be/sciences/biologie/urbm/bioinfo/esypred/ I-TASSER http://zhang.bioinformatics.ku.edu/I-TASSER/ WHATIF (www) http://swift.cmbi.ru.nl/servers/html/index.html CPHmodels 3.0 (www) http://www.cbs.dtu.dk/services/CPHmodels MODELLER 9v6 (standalone for windows, mac, linux; also web submission) http://www.salilab.org/modeller/

8. Increase in sequence identity correlates with increase in structural similarity RMSD of corea-carboncoordinates for two homologous proteins sharing 50% identity expected at ~1? (GLY 3.5?, helix 5? diameter) Theoretical models are low resolution, and depend on quality of input alignment!

9. Sequence alignment is the single most important step in homology modeling. Lab 10.2 9 Where are we with respect to our objectives ?Where are we with respect to our objectives ?

10. Important terminology The protein(s) whose structure(s) is/are already known are referred to as the "reference", "real", or ?template? protein(s). The protein whose structure you are trying to build is called the "model", "unknown", or "target" protein.

11. Lab 10.2 11 Alignment is the limiting step for homology model accuracy

12. What can be Modeled?

15. Web-based homology modeling

16. Swiss-Model

17. Lab 10.2 17 Swiss-Model steps:

18. Lab 10.2 18 Swiss-Model steps:

19. Lab 10.2 19 Swiss-Model steps:

20. Lab 10.2 20 Swiss-Model steps:

21. Lab 10.2 21 Swiss-Model steps:

22. Lab 10.2 22 Swiss-Model steps:

23. Lab 10.2 23 Swiss-Model steps:

24. Lab 10.2 24 Swiss-Model steps:

25. Lab 10.2 25 Swiss-Model steps:

26. Lab 10.2 26 Swiss-Model comparison

27. The Swiss-Model Workspace

28. The Swiss-Model: Your own Workspace

29. The Swiss-Model Workspace

45. Tutorial Exercise 1 UniProt entry Q11CR8_MESSB (NCBI entry YP_675972) is described as a "Fructose-bisphosphatealdolase class 1, from Mezorhizobium sp. (strain BNC1)? UniProt Homepage: http://www.uniprot.org/ NCBI Homepage: http://www.ncbi.nlm.nih.gov/ It belongs to Pfam (http://pfam.sanger.ac.uk/) PF00274, the Fructose-1,6-Bisphosphate Aldolases (Class 1); this family contains 23 PDB structures. When we run BlastP on Q11CR8_MESSB against PDB, we get hits to all these structures; %ids range from 48 to 54%, which is reassuringly high. Let?s try SwissModel in Automated mode: http://swissmodel.expasy.org/workspace Pfam- Even though the page says 91 structures, 23 distinct protein structures. To Blast: Get Fast sequence from UniProt server Then, use NCBI blast against PDB. It will get 23 structures with very low E-value. Save this structure. Pfam- Even though the page says 91 structures, 23 distinct protein structures. To Blast: Get Fast sequence from UniProt server Then, use NCBI blast against PDB. It will get 23 structures with very low E-value. Save this structure.

46. Tutorial Exercise 2 Again, let?s try SwissModel in Automated mode for the following: http://swissmodel.expasy.org/workspace >976347 Human zinc finger homeodomain protein KPFRCEVCNYSTTTKGNLSIHMQSDKH ? The steps involved in this process may be: First, let?s use the automated mode of Swiss-model to model this protein. Pfam- Even though the page says 91 structures, 23 distinct protein structures. To Blast: Get Fast sequence from UniProt server Then, use NCBI blast against PDB. It will get 23 structures with very low E-value. Save this structure. Pfam- Even though the page says 91 structures, 23 distinct protein structures. To Blast: Get Fast sequence from UniProt server Then, use NCBI blast against PDB. It will get 23 structures with very low E-value. Save this structure.

52. Model Assessment

53. Model Assessment ? cont.

54. Model Assessment Output

60. Arne Elofsson (arne@bioinfo,se)? Swiss-PdbViewer - DeepView

62. Further Details DeepView tutorial http://au.expasy.org/spdbv/text/tutorial.htm Advanced tutorial on Swiss-Model &DeepView http://www.usm.maine.edu/~rhodes/SPVTut/text/HGHomMod.html

63. Suggested Reading Swiss-Model?sadvice: http://www.expasy.org/swissmod/SM_ModelAccuracy.html A goodinteractivetutorial on ProteinModelling: http://www.ncbi.nlm.nih.gov/Class/minicourses/x1a.html

65. Demonstrations Now let?s assess our two complete models: Go to [Tools] >> Structure Assessment on Swiss-Model, and upload each model in turn: Add Whatcheck and Procheck to the selection, and add the resolution (check result file for automated mode, or check PDB website for alignment mode) Also, go to the SolvX Server and input our models. It should give us (at least) two graphs per input ? the first will be our model, the other(s) our template(s). Automated mode ? 1.88A Alignment mode ? 1.80AAutomated mode ? 1.88A Alignment mode ? 1.80A

66. Demonstrations What validation checks are the important ones? Whatcheck: Accessibility-related (2.6), 3D-Database (2.8), Geometric (2.5.4 2.5.12 2.5.13 2.5.14) Checks. Make a note of bad residues and regions. Procheck: Residues Report (G-factors) and Ramachandran Plot. Again, note bad residues and regions. SolvX: Compare your model with the template(s). Where are the worst (most solvent accessible) regions? Note them down. How does your alignment model for ALF1_STACA compare with your neighbor's model?

67. Procheck Results Demo 1 Q11CR8_MESSB Structure Model Demo 2 Q07159 Structure Model

68. Solvation Profile Demo 1 Q11CR8_MESSB Structure Model Demo 2 Q07159 Structure Model

69. Demo 2 Q07159 Structure Model Use 1EPXA as a template Use 2IQTA as a template


Other Related Presentations

Copyright © 2014 SlideServe. All rights reserved | Powered By DigitalOfficePro