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DockoMatic : Automated Tool for Homology Modeling and Docking Studies

Tutorial. DockoMatic : Automated Tool for Homology Modeling and Docking Studies. Learning Objectives. I. Create & validate a protein homology model II. Use molecular docking to calculate the binding energy for a drug to the protein III. Assessment of docking results

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DockoMatic : Automated Tool for Homology Modeling and Docking Studies

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  1. Tutorial DockoMatic:Automated Tool for Homology Modeling and Docking Studies DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  2. Learning Objectives • I. Create & validate a protein homology model • II. Use molecular docking to calculate the binding energy for a drug to the protein • III. Assessment of docking results • IV. Visualize the protein-drug complex DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  3. Systems of Interest • Protein: Collagen α1 (XI) NPP domain • 223 amino acid protein • 2 disulfide bonds • A minor fibrillar collagen involved in thrombosis • Drug: Arixtra (a.k.a. Fondaparinux) • A heparin-based drug • An anticoagulant used to treat blood clots • Binds Col α1 (XI) NPP to prevent blood coagulation Arixtra structure DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  4. DockoMatic 2.0 • User friendly graphical user interface (GUI) for automation • Homology model creation using the Timely Integrated Modeller (TIM) interface • Create, submit, manage AutoDock1 molecular docking calculations • Track jobs & analyze results using PyMol2 DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking 1. Morris, G. M. et al. J. Computational Chemistry 2009, 16: 2785-91. 2. The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC.

  5. How many structures solved? The Protein Data Bank* *Bernstein, et al. (1977) J. Mol. Biol. 112, 535. DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  6. Part I: Homology Modeling DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  7. Homology Modeling: Overview • Prediction of 3D-structure of a given protein sequence (target) based on alignment to known protein structures (templates) • A useful model requires 30% sequence identity between target and template • Models used to understand function, activity, ligand binding paradigms in drug design, etc. DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  8. Begin with the target amino acid sequence Use the Basic Local Alignment Search Tool* (BLAST) to search for amino acid sequences of template proteins where the 3D structure is available The principle repository for 3D protein structures is the National Center for Biotechnology Information+ (NCBI) Only amino acid sequences with greater than 30% identity between target and template should be considered. If functionality is known for a class or family of proteins, look to protein templates with similar functionality as the target. Homology Model: Template Selection *Johnson et al. (2008) Nucleic Acids Res. 36, W5-9. +Edgar, et al. (2002) Nucleic Acids Res. 30, 207-210 DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  9. Homology Modeling: Flow Chart Known (Template) Structures NO YES Target Sequence Template Selection Evaluate the Model Homology Model Alignment (Target-Template) Model Building for the Target DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  10. Homology Model Creation: DockoMatic Procedure DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  11. Open Terminal Window DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  12. Type: ssh –X username@host DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  13. Enter password DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  14. This is the HOME directory DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  15. Type: cd $SCRATCH DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  16. Type: mkdir DOCKOMATIC-WORKSHOP Type: cd DOCKOMATIC-WORKSHOP Type: dockomatic DockoMatic will now open in a new window DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  17. DockoMatic 2.0 GUI DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  18. DockoMatic • Select: Use Modeller DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  19. DockoMatic: Accessing the TIM Wizard • Click on: Receptor • Timely Integrated Modeller (TIM) Wizard will open in a new window DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  20. DockoMatic – TIM Wizard Interface • TIM Wizard DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  21. TIM Step 1: Enter Template Sequence • Click on: Output Directory DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  22. TIM Step 1 (cont’d): Sequence Entry • Select: The desired output directory • Click: OK DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  23. TIM Step 1 (cont’d): Sequence Entry • Output directory path is now established • Note this path for future reference DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  24. TIM Step 1 (cont’d): Sequence Entry • Click on: ‘Sequence’ Choose the target .pdb file OR • Copy/Paste Sequence: If you don’t have a .pdb, you can copy & paste the sequence here. DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  25. TIM Step 1 (cont’d): Sequence Entry • Name the target sequence • Click: Next DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  26. TIM Step 2: Search for a Template • BLAST Template Search DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  27. TIM Step 2 (cont’d): Template List • Template list • BLAST output DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  28. TIM Step 2 (cont’d): Template Selection • Select a template • Templates listed from highest match to lowest • Click: Next DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  29. TIM Step 3: Sequence Alignment • Alignment in progress DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  30. TIM Step 3: Select Aligned Sequence • Select sequence of template that has been aligned with the target DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  31. TIM Step 4: Edit Aligned Sequence • Aligned template and target sequence display. • Alignment may be edited in this window. • Click: Next DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  32. TIM Step 5: Model Generation • Model generation in progress DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  33. TIM Step 5: List of Models Created • List of homology models for target protein created based on template structure DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  34. TIM Step 5: Select Homology Model • Select a homology model • Models listed from best to worst correlation • Click: Finish DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  35. End TIM Wizard: 3D Model for MD • Receptor field shows selected homology model. • Do not close this window; it will be required for molecular docking. DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  36. Location of Model Structure Files Open a terminal window. Enter output directory path (you noted this earlier). Type: ls The content of the working directory contains the .pdb files of the homology models for the target protein along with all other output files generated by DockoMatic. DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  37. Homology Model Validation DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  38. HM Validation: Ramachandran Plot • Model assessment using RAMPAGE1webserver DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking 1. http://mordred.bioc.cam.ac.uk/~rapper/rampage.php

  39. HM Validation: Sequence Alignment DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  40. HM Validation: Structure Overlay PDB ID: 2UUR Template Homology model for Col α1 (XI) NPP Root mean square deviation of Cα atoms = 1.12 Å DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  41. Part II: Grid Parameter File Creation DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  42. Open AutoDockTools(ADT) In the terminal type: adt & Click on the Icon created at installation DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  43. Click on: Grid Then click ‘Macromolecule’ in the popup menu, then ‘Open…’ You can either load a .pdb or a .pdbqt created from an earlier ADT use. Change the file type to ‘.pdb’, unless loading the .pdbqt file type. Choose your file, then click open. DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  44. The file will load then imidiately ask you to choose a location to save the converted .pdbqt Choose your location and filename, then click save DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  45. Click on: Grid Then click ‘Grid Box…’ in the popup menu This allows you to define the area of interest in the molecule. It is described by xyz coordinates. The molecule can be rotated by clicking and dragging. DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  46. Click on: Grid Then click ‘Output’ in the popup menu, then ‘Save GPF…’ Choose your location and filename, then click save DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  47. Part III: Molecular Docking DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  48. Molecular Docking: Background • Docking : Molecular simulation of a ligand binding to a receptor • Output: Binding energies & scoring functions • Visualization: Binding poses for ligands • Docking tools • AutoDock • DOCK • Glide • MOE • GOLD DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

  49. Force Fields for Autodock Energy Function ΔGvdW= WvdW ∑i, j ( Aij / rij12- Bij / rij6 ) ΔGH-bond = WH-bond ∑i, jE(t) * ( Cij / rij12 - Dij / rij10 + Ehbond ) ΔGelec = Welec ∑i, j ( qi * qj ) / ( ε(rij) * rij ) ΔGtor = WtorNtor ΔGdesolv = Wdesolv ∑i (C), j (Si *Vj * exp ( -rij2 / (2 * σ2) ) ) ΔG = ΔGvdW+ ΔGH-bond+ ΔGelec+ ΔGtor+ ΔGdesolv DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking http://autodock.scripps.edu/resources/science/equations/

  50. Molecular Docking: Protocol http://Autodock.scripps.edu DOCKOMATIC-Student Procedure-Homology Modeling & Molecular Docking

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