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Swiss-PdbViewer Introduction-Wenwen Wang
- 1. Swiss-PdbViewer Wenwen Wang E-mail: wenwenwang@gmx.de Wenwen.Wang@anatomie.med.uni-giessen.de Dec. 2012
- 3. 1. Download and Install • Downloading the PDB files in your own PC PDB home page http://www.rcsb.org/pdb/home/home.do • Downloading Swiss-PdbViewer http://spdbv.vital-it.ch/download.html
- 4. Protein structure database: Protein data bank (PDB) • The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography or NMR spectroscopy • The PDB is a key resource in areas of structural biology. http://www.pdb.org/pdb/home/home.do
- 5. Get your target protein in PDB Example : thymidine kinase (TK) 1 2
- 6. Query Parameters Protein name Source Organism Methods Chemical Components
- 7. Structure Entity Hits 29 entries available PDB ID of this entry TK from virus with ligand (substrate) X-ray crystallography
- 8. Structure and related data (1KIM) Related data on each tag The citation of this entry Visualization of biological assembly
- 10. Sequence data (1KIM) Sequence ID of 1KIM in UniProtKB
- 11. Thymidine kinase thymidine + ATP = thymidine 5'-phosphate + ADP
- 12. Download protein structure file from PDB 1.Save the file in your PC 2.Open the file by PbdViewer
- 13. Download and Install PdbViewer • Download Swiss-PdbViewer http://spdbv.vital-it.ch/download.html • Download user guide http://spdbv.vital-it.ch/Swiss-PdbViewerManualv3.7.pdf • Tutorial video (English) http://www.youtube.com/watch?v=nYT5qwtfNew&feat ure=related http://www.youtube.com/watch?v=yFE3CAHNkZg
- 14. Web page
- 15. Install and Run Swiss-PdbViewer
- 16. File Operations
- 17. 2. Workspace Layer info Toolbar Control Panel
- 18. 3. Control panel van der Waals dots spheres C-white O-red N-blue S-yellow P-orange H-cyan Other-gray
- 19. 3.1 Selection
- 22. 3.2 Render in Solid 3D
- 23. 4. Tools Center Enlarge Translate Rotate Distance between 2 atoms Angle between 3 atoms omega, phi and psi angles Identify atoms Display groups that are at a certain distance from a selected atom Center the molecule on one atom Fit a molecule onto an other Mutation Torsion
- 24. 4.1 Measure distance between 2 atoms ---Open 1CRN ---Select ---Group Kind ---SS bonds ---Show only ---Side chain ---Label ---Measure the distance between 2 Cα of Cys which have disulphide bonds ---Pick 1st atom ---Pick 2nd atom ---Hit “Esc”
- 25. 4.2 Measure Angle between 3 atoms ---Press button ---pick center atom ---pick 2nd atom ---pick 3rd atom ---Esc 1 3 2
- 26. 4.3 Measure of omega, phi and psi angles of the picked amino-acid ---Press “Ctrl” key + button ---pick 4 atoms ---measure the torsion angle of any specific bond ---Esc1 2 3 4
- 27. 4.4 Provenance of an atom
- 28. 4.5 Mutations
- 29. 4.5 Mutations
- 31. 4.5 Mutations
- 32. 4.6 Torsions ---Open---1KIM ---select THM1 ---only show THM1 ---label it ---color it orange ---Zoom in & Center ---render in solid 3D ---select one atom and display groups at 6A ---Show & Center ---col---white ---THM1 orange ---Tool ---Compute H-Bonds ---Display ---Show H-Bonds Distance ---only select THM1 ---Show Only H-Bonds from Selection ---Select ---Pick on Screen ---Gln125 & Tyr101 ---color them blue ---Torsion ---pick one atom ---pick 2nd atom
- 34. 5.1.1 Coloring Chain acting on Ribbon 1-OR -color -ribbon 1 2
- 35. Chain A Chain B Chain C Chain D 5.1.1 Coloring Chain acting on Ribbon
- 36. Chain A Chain B Chain C Chain D 5.1.2 Coloring Chain acting on Backbone
- 37. OR -color -ribbon 1 2 5.2.1 Color B-factor acting on Ribbon
- 38. 5.2.1 Color B-factor acting on Ribbon
- 39. 1-OR -color -backbone 1 3 2 5.2.2 Color B-factor acting on Backbone
- 40. 5.2.2 Color B-factor acting on Backbone
- 41. OR -color -ribbon 1 2 5.3 Color in Residue Type acting on Ribbon
- 42. 5.3 Color in Residue Type acting on Ribbon Type: Gray-non polar amino acid: Val, Leu, Pro, Ala, Trp, Gly, Met, Phe, Cys, Ile Yellow-polar amino acid: Ser, Thr, Asn, Try, Gln Red-negtive charge (acid amino acid): Asp, Glu Blue-positive charge (basic amino acid): Lys, His, Arg
- 43. 5.4.1 Color Secondary Structure acting on Ribbon
- 44. 5.4.1 Color Secondary Structure acting on Ribbon
- 45. 5.4.2 Color Secondary Structure Succession
- 46. 5.4.2 Color Secondary Structure Succession
- 47. 6.1 Enzyme-ligand interaction---Merging ---Loading PDB file of protease ---Color---Chain ---Loading PDB file of inhibitor ---Merging 2 layers ---Alignment window---select protease--- Select---All ---select inhibitor ---Edit---Create Merged Layer from Selection (by layer)
- 48. 6.2 Enzyme-ligand interaction---Active site ---display only groups that are within 10A of the center atom of inhibitor ---Center the molecule ---label them ---Tools ---Compute H- Bonds
- 49. 6.2 Enzyme-ligand interaction---Active site ---select I121145 in Control Panel ---Display ---Show Only H- Bonds from Selection 1 2
- 50. 6.2 Enzyme-ligand interaction---Active site ---remove the other labels, only label residues interact with inhibitor, and color them pink ---Display ---Show H- Bonds Distances
- 51. 7.1 Structural Alignment-Magic Fit ---Loading sars.pdb ---Loading IBV.pdb ---Color---Layer ---click the reset- view button ---Wind ---Alignment ---Fit ---Iterative Magic ---aligned residues are shaded in gray ---show structures in ribbon 1 2 34
- 52. 7.2 Structural Alignment-show in Ribbon 5
- 53. 7.3 Structural Alignment vs Sequence Alignment
- 54. 8.1 Homology Modeling: register with Swiss- Model http://swissmodel.expasy.org/workspace/index.php?func=account_create1
- 58. 8.4 Load template structure ---loading raw amino acid sequence: Murine_HV.fasta ---loading SARS protease with known 3D structure: 2h2zA.pdb 2h2zA Murine_HV
- 60. 8.6 Adjusting manually 31 2 4 5 “Ctrl + space bar”
- 63. 8.8 Template vs Model 2h2zA Murine_HV