1 / 53

Docking molecules with Vina

Docking molecules with Vina. Autodock Vina. To study molecules they must be docked. Docked molecules bind their enzyme or receptor in a specific conformation Docked molecules bind with high affinity The best way to get docked conformation is to use X-ray crystallography

bobby
Download Presentation

Docking molecules with Vina

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Docking molecules with Vina

  2. Autodock Vina

  3. To study molecules they must be docked • Docked molecules bind their enzyme or receptor in a specific conformation • Docked molecules bind with high affinity • The best way to get docked conformation is to use X-ray crystallography • Alternative: use docking software like Vina to predict docked conformation

  4. What is docking? • Find the conformation with which a ligand binds a receptor • This information includes full coordinates of all ligand atoms • The docked configuration is the (presumed) lowest energy binding site

  5. Steps • 1. get protein structure • 2. create files with protein only • 3. Use a known ligand (not your ligand) to define the ligand binding site • 4. Generate some modified structure files • 5. Use files with docking software • 6. Extract predicted conformation and make new file with protein and target ligand docked

  6. Make a folder • Need a place to store many files • Make c:\thesis

  7. Get PDB file • Go to PDB RSCB on web • Search for PDB code if unknown • Once PDB code is known, download it • Use PDB/Tools, download entries and follow instructions • You must have Java enabled • Change mmCIF to PDB as type of file • Change compressed to uncompressed • Save in your thesis folder

  8. PDB search

  9. PDB download

  10. PDB info – Protein name

  11. PDB – ligand name (HET)

  12. PDB coordinates

  13. Start with PDB file with protein and ligand (not your ligand) • Make a copy of the PDB file • Split it into only protein and only ligand • Ligand will be used to get coordinates of binding site • Example: beta adrenergic receptor and carazolol • 2rh1.pdb

  14. Use wordpad text editor • Copy cau (= carazolol, ligand) from 2rh1 • Paste into a file called car.pdb • REMARK carazolol • HETATM 3598 O17 CAU A 408 -33.477 10.957 8.170 1.00 50.96 O • HETATM 3599 C16 CAU A 408 -32.267 10.230 8.041 1.00 45.65 C • HETATM 3600 C18 CAU A 408 -32.478 8.951 7.225 1.00 51.24 C • HETATM 3601 N19 CAU A 408 -33.702 8.250 7.600 1.00 54.99 N • HETATM 3602 C20 CAU A 408 -33.806 6.805 7.498 1.00 60.13 C

  15. PDB files have 3D structure information including XYZ coordinates of atoms • Also have atom numbers • Residue numbers • Atom types

  16. Find the center of the ligand • This will be the center used when you dock your ligand to the receptor • Start with the X coordinate. Add all the X values and then divide by the number of atoms. Record for later • Repeat for Y and Z coordinates • The only purpose of having a ligand at this point is to define the ligand binding site.

  17. Find coordinates • z • y • x • REMARK carazolol • HETATM 3598 O17 CAU A 408 -33.477 10.957 8.170 1.00 50.96 O • HETATM 3599 C16 CAU A 408 -32.267 10.230 8.041 1.00 45.65 C • HETATM 3600 C18 CAU A 408 -32.478 8.951 7.225 1.00 51.24 C • HETATM 3601 N19 CAU A 408 -33.702 8.250 7.600 1.00 54.99 N • HETATM 3602 C20 CAU A 408 -33.806 6.805 7.498 1.00 60.13 C

  18. Carazolol – no hydrogens

  19. Visualizing structures • Try rasmol or raswin • Download at google: rasmol bernstein • Several web tutorials available

  20. Adding hydrogens • Hydrogen is rarely found in PDB files • But all atoms are needed to dock molecules • Solution: add back missing hydrogens • We will use Babel

  21. OpenBabel • Download openbabel from its web site • Install • Use the command prompt to run the program • Use a full ‘path’, that is a description of the program location • Add hydrogens • On my machine that is (one line): • \lm\downloads\openbabel-2.1.1\babel.exe -ipdb car.pdb –opdb carH.pdb -h

  22. Add H

  23. Check that hydrogens have been added • HETATM 20 C1 CAU 408 -26.395 6.432 7.689 1.00 0.00 C • HETATM 21 C6 CAU 408 -27.717 6.731 8.006 1.00 0.00 C • HETATM 22 C5 CAU 408 -28.269 7.948 7.652 1.00 0.00 C • ATOM 23 H CAU 408 -34.319 10.255 8.260 1.00 0.00 H • ATOM 24 H CAU 408 -31.904 9.929 9.079 1.00 0.00 H • ATOM 25 H CAU 408 -31.591 8.256 7.396 1.00 0.00 H

  24. Other ligands • Up to now we have been dealing with the ligand found in the PDB file with your receptor/protein • You may wish to try docking that ligand as a control • At some point you will want to deal with other ligands

  25. Getting other ligands • To use ligands they must be transferred from the page to PDB format • Some ligands may be present in other files in the protein data bank – try searching • Ligands can be drawn, e.g. with DS Viewer Pro or other software and saved in PDB format • Most ligand files will have to have hydrogens added

  26. Add hydrogen to the protein • Repeat ligand procedure, but with protein • We did car.pdb  carH.pdb • Now make copy of the protein pdb file with the ligand deleted (e.g. CAU in this example) • (you can delete WAT and other ligands too) • Now, with full path, use babel to add H

  27. Add hydrogen to protein • Full path on my machine (yours will differ) • \lm\downloads\babel-2.1.1\babel.exe –ipdb bar.pdb –opdb barH.pdb -h • Result: bar.pdb  barH.pdb

  28. We’re almost ready to dock • But we need two things: • Torsions • Hydrogen bonds

  29. Torsions • The ligand may have rotatable bonds • Benzene can not twist (0 torsions) • Hexane can twist (3 torsions, we’ll ignore rotating methyl groups) • MGLtools calculates these • Vina will twist the ligand to try to find the best fit during docking

  30. H bonds • We need to find H bond acceptors and donors • MGLtools also calculates these

  31. MGLtools • MGLtool, ADT, Autodock tools are the same • Download from MGLtools site • Install • Read tutorial • Click to open window

  32. MGLtools

  33. MGLtools We will use MGLtools/Autodock tools for two things: Annotate the ligand(s) Annotate the receptor

  34. Autodock / MGL tools • First we will process the ligand to add torsions and H bond information • On left side of ADT screen find ligand menu • Open ligandH.pdb (or other file) • Note: this is the ligand file you want to dock, not the X-yl structure file, unless you are docking it as a control

  35. Autodock/MGLtools and ligand • Select torsion tree • Find the ligand torsion ‘root’. Detect root • Aromatic carbons: set names • Output: Save file as carH.pdbqt • It is key that you save the pdbqt file that MGLtools makes

  36. ADT and protein/receptor • Find ‘grid’ menu • Macromolecule • Open receptor file with hydrogens (receptorH.pdb) • The file gets processed • Save as ligandH.pdbqt • Do not choose ‘flexible’

  37. ADT receptor refinement • Now the receptor file and ligand file have been saved as .pdbqt files. • These have H bond and torsion information • Look at the ligandH.pdbqt file using wordpad or simpletext • It still looks like a .pdb file, but has extra information added

  38. Now we have all of the files that we need to dock a ligand • Let’s check: • receptorH.pdbqt • ligandH.pdbqt • Binding site coordinates

  39. Setting up Vina • Vina needs to know what you want to do: • What receptor • What ligand • Where the binding site is • Where to send out the results • This information is placed in a file called config.txt

  40. Configuration file, config.txt • Config.txt gives information to Vina as it docks your ligand • The left side of each = is Vina code (don’t change) • The right side of each = is your input • You control the site of binding, the size of the site, and the receptor and ligand

  41. Example Vina configuration file out = out_carh.pdbqt receptor = 2rhe.pdbqt ligand = carh.pdbqt center_x = -28 center_y = 9 center_z = 6 size_x = 25 size_y = 25 size_z = 25 energy_range = 4

  42. Download Vina • Web site AutoDock Vina • Install in ‘thesis’ folder, or wherever your config file and .pdbqt files are saved. • Get the right version of Vina for your computer (e.g. PC vs. Mac)

  43. Autodock Vina

  44. Read manual!

  45. Dock ligand • Open command prompt • Make certain that command prompt is pointed to thesis directory/folder • Use the cd command with command prompt or Mac command screen

  46. Finding the right directory • If necessary change directory using ‘cd’ • E.g. type ‘cd \thesis’ [without the quotes] for a PC • Or type ‘cd /thesis’ [without quotes] for mac • This assumes that you put all your files in the directory ‘thesis’ on the c:drive or equivalent • Type dir/p [PC] or ls [Mac] to check that your files are present

  47. Vina docking To dock, type : vina.exe --config config.txt

  48. Vina docking

  49. Vina output • It takes a minute or two for Vina to dock • This represents millions of docked positions being analyzed • The output file name is defined by the config file out = outfilename.txt • Each outfile has several models • We usually only care about model 1, the best

  50. Output score • We often want to know how tightly a ligand binds • Vina gives an estimate in the output file • Look for Vina Result: x • If x is -10 or less, binding is very tight • If x is -6 to -7 binding is just random, not tight • In between is hard to judge

More Related