Tutorial. Docking School SAnDReS Tutorial Cyclin-Dependent Kinases with K i Information (Docking Hub)

Transcription

1 Tutorial Docking School SAnDReS Tutorial Cyclin-Dependent Kinases with K i Information (Docking Hub) Prof. Dr. Walter Filgueira de Azevedo Jr. Laboratory of Computational Systems Biology azevedolab.net azevedolab.net walter@azevedolab.net 1

2 Docking Hub 2

3 Docking Simulations-AutoDock 4 We can run AutoDock 4 (Morris et al., 1998) AutoDock Vina (Trott & Olson, 2010), and Molegro Virtual Docker (Thomsen&Christensen,20 06). directly from SAnDReS. To run AutoDock 4 and AutoDock Vina using SAnDReS, you need to have prot.pdbqt and lig.pdbqt files for each structure in the dataset. We may use AutoDockTools (Morris et al., 2009) to generate the PDBQT files. 3

4 Docking Simulations-AutoDock 4 We may follow this another tutorial here to learn how to use AutoDockTools to generate PDBQT from PDB files. Here we have the files generated by SAnDReS for each structure in the dataset. Use prot.pdb and lig.pdb files to generate you PDBQT files. 4

5 Docking Simulations-AutoDock 4 Consider that you have generated the PDBQT files for the structures 1E1V in the dataset, as shown here. 5

6 Docking Simulations-AutoDock 4 To run docking simulations, click on Docking Hub- >Docking Simulations, as shown here. 6

7 Docking Simulations-AutoDock 4 On the new pop-up window, click on the AutoDock 4 button. 7

8 Docking Simulations-AutoDock 4 Please make reference to AutoDock 4 paper when using this program. Click on the OK button. 8

9 Docking Simulations-AutoDock 4 On this new pop-up window, we have the map to carry out docking simulations using AutoDock 4. First, we click on the AutoGrid button. 9

10 Docking Simulations-AutoDock 4 Click on the Yes button. 10

11 Docking Simulations-AutoDock 4 If everything goes fine, we get the following message: autogrid4: Successful Completion.. Now we click on the Set Up DPF button. 11

12 Docking Simulations-AutoDock 4 On this new pop-up window, we may select the docking parameters. For instance, the search algorithm. AutoDock 4 is able to run four different algorithms: Lamarckian Genetic Algorithm (LGA), Genetic Algorithm (GA), Local Search (LS), and Simulated Annealing (SA). In addition, we may also calculate scoring function values for the crystallographic position of the ligand clicking on the Energy for PDB button. 12

13 Docking Simulations-AutoDock 4 The details for each algorithm can be modified on this window. The values shown here are taken from the default values indicated on the AutoDock user guide. For this tutorial, we will use the default values. Click on the Save DPF button. SAnDReS will generate the docking.dpf file, which will be used to run AutoDock 4. The docking.dpf file has all parameters necessary to run AutoDock 4. We may edit it by clicking on the Open DPF button. Click on the Close button to proceed. 13

14 Docking Simulations-AutoDock 4 Now we can perform the docking simulation using AutoDock 4, click on the AutoDock button. 14

15 Docking Simulations-AutoDock 4 Click on the Yes button. 15

16 Docking Simulations-AutoDock 4 It may take few minutes. Let s enjoy the music 16

17 Docking Simulations-AutoDock 4 Once finished, SAnDReS shows the following message: autodock4: Successful Completion on.we may now carry out the analysis of docking results. Click on the Analysis button. 17

18 Docking Simulations-AutoDock 4 Click on the Yes button. 18

19 Statistical Analysis of Scoring Functions vs RMSD What SAnDReS is actually doing is running the input file strmsd.in, shown here. This input file was automatically generated by SAnDReS. The strmsd.in file has two lines only. The first line brings the keyword STRMSD, followed by the CSV file name (redock_autodock.csv) and the headers. The number before each header indicates the column for this header. For instance, 2, RMSD, indicates that the column for RMSD is the second column. The last line is the ENDOF line. The redock_autodock.csv file brings the energy terms for AutoDock scoring function and docking root mean square deviation (RMSD) related to crystallographic position of the ligand (lig.pdbqt). redock_autodock.csv strmsd.in STRMSD,redock_autodock.csv,2,RMSD,3,FreeEnergy,4,FinalIntermolecularEnergy,5,vdW+Hbond+desol venergy,6,electrostaticenergy,7,finaltotalinte rnalenergy,8,torsionalfreeenergy ENDOF Model,RMSD,FreeEnergy,FinalIntermolecularEnergy,vdW+Hbond+desolvEnergy,ElectrostaticEnergy,Fin altotalinternalenergy,torsionalfreeenergy 10,4.23,-6.68,-7.87,-7.71,-0.16,-0.33,1.19 5,4.75,-6.56,-7.75,-7.41,-0.34,-0.4,1.19 6,1.06,-6.35,-7.55,-7.59,0.04,-0.27,1.19 3,1.07,-6.34,-7.53,-7.62,0.09,-0.31,1.19 1,1.06,-6.33,-7.52,-7.61,0.09,-0.33,1.19 4,1.11,-6.31,-7.51,-7.61,0.1,-0.4,1.19 7,1.13,-6.3,-7.49,-7.6,0.11,-0.4,1.19 2,1.10,-6.28,-7.48,-7.57,0.09,-0.4,1.19 9,2.07,-6.14,-7.34,-7.68,0.35,-0.58,1.19 8,2.05,-6.13,-7.32,-7.62,0.3,-0.54,

20 Docking Simulations-AutoDock 4 SAnDReS evaluates the correlation between energy terms of the AutoDock scoring function and docking RMSD, as shown here. These results are in the strmsd.log and strmsd.csv files. SAnDReS also creates a two-column CSV file for each term of the AutoDock scoring function. In these files, the first column is for the docking RMSD of each pose and the second column is for energy value of each pose. 20

21 Docking Simulations-AutoDock 4 SAnDReS created a new directory name LGA, since we run the LGA search algorithm. The LGA directory is on C:\Users\Walter\Desktop\T 001\Dataset_2017_02_22_ 12_17_48\1E1V. If we run GA search algorithm, the results will be on the GA directory and so on. 21

22 Docking Simulations-AutoDock 4 To prepare files to generate scatter plots, click on Prepare Files to Plot button. 22

23 Docking Simulations-AutoDock 4 We have a new pop-up window, where we can define the plot parameters. To generate the files, click on the Generate Files button. Then click on the Close button. 23

24 Docking Simulations-AutoDock 4 To plot, click on the Plot button. 24

25 Docking Simulations-AutoDock 4 Click on the Plot pltcsv File button. 25

26 Statistical Analysis of RMSD x Scoring Functions What SAnDReS is actually doing is running the pltcsv_00.in input file, that was automatically generated using the information selected in Parameters for Scatter Plot window. Here we have a description of the fields, that are separated by comma. Keyword to plot File to plot Type of plot xmin xmax ymin ymax x-axis label y-axis label Title PLTCSV,strmsd004.csv,SCATTER,0.0,12.0,-1.0,-0.0,Docking RMSD ($\AA$),FinalTotalInternalEn,FinalTotalInternalEn vs Docking RMSD ($\AA$),o,k,PNG,1,NOTEXT,True,300,50.0 Marker size (pixels) Plot DPI Flag for Grid (False means no grid) To include correlation and p-value information into the plot (can be TEXT or NOTEXT) Polynomial degree to be used in the best fit curve Plot format Point colors Marker to plot 26

27 Docking Simulations-AutoDock 4 SAnDReS generated a scatter plot, as shown here. Close the plot window and click on the Close button. 27

28 Docking Simulations-AutoDock 4 The rest of the buttons may be used to access tutorials, a manual, and the SAnDReS site. Click on the Close button. 28

29 Docking Simulations-AutoDock Vina To run docking simulations, click on Docking Hub- >Docking Simulations, as shown here. 29

30 Docking Simulations-AutoDock Vina On the new pop-up window, click on the AutoDock Vina button. 30

31 Docking Simulations-AutoDock Vina Click on the OK button. 31

32 Docking Simulations-AutoDock Vina To run AutoDock Vina we need the config.txt file. This file was generated for each structure in the dataset when we previously run Pre- Docking-> Generate Binding Site for Crystallographic Structures. To be sure, click on the Edit config.txt button. 32

33 Docking Simulations-AutoDock Vina As we can see, we have the config.txt file. Don t forget, we also need prot.pdbqt and lig.pdbqt files. We may use AutoDockTools to generate the PDBQT files. We may follow the tutorial available here to learn how to use AutoDockTools to generate PDBQT from PDB files. Click on the Close button. 33

34 Docking Simulations-AutoDock Vina To run AutoDock Vina, click on the Run Vina button. 34

35 Docking Simulations-AutoDock Vina Click on the Yes button. 35

36 Docking Simulations-AutoDock Vina It may take few minutes. Let s the music play 36

37 Docking Simulations-AutoDock Vina Once finished, SAnDReS shows the following message: SAnDReS finished running AutoDock Vina!, as shown here. We may carry out analysis of the docking results as previously described for AutoDock 4. Click on the Close button. 37

38 Docking Simulations-Molegro Virtual Docker To run Molegro Virtual Docker (MVD) from SAnDReS, you need to have MVD installed on your computer. MVD doesn t come along with SAnDReS. You also need the system.mvdml file. To create the system.mvdml file, you should go the Dataset directory, for instance, here our structures are all on C:\Users\Walter\Desktop\T 001\Dataset_2017_02_22_ 12_17_48. 38

39 Docking Simulations-Molegro Virtual Docker As we can see here, we have one directory for each structure. If we click on one of these directories, for instance 1E1V, we have all structure files related to the structure 1E1V. 39

40 Docking Simulations-Molegro Virtual Docker What we have on the directory 1E1V are shown here. We open the structure 1E1V_CMG_H2O.pdb with MVD. Once loaded, we click on Preparation- >Detect Cavities->OK. The program MVD automatically detect potential binding pockets on the structure. Then we save our structure clicking on File->Save Workspace as... We save the system as system.mvdml. For more information about MVD, click here. 40

41 Docking Simulations-Molegro Virtual Docker As we can see here, we have created the system.mvdml file. Now we should create 32 new directories, named P01- P32. On each directory, we should have a copy of the system.mvdml file. 41

42 Docking Simulations-Molegro Virtual Docker So, we ended up with all 32 directories, one for each docking protocol. SAnDReS needs theses directories. It is where SAnDReS will look for the system.mvdml file and also where the result files will be written. 42

43 Docking Simulations-Molegro Virtual Docker To run docking simulations, click on Docking Hub- >Docking Simulations, as shown here. 43

44 Docking Simulations-Molegro Virtual Docker On the new pop-up window, click on the Molegro Virtual Docker (MVD) button. Don t forget, you should have Molegro Virtual Docker (MVD) installed on your computer to use SAnDReS to carry out docking simulations using MVD. In addition, you also need to have system.mvdml file for each structure in the dataset. These files should be on new directories named from P01 to P32 for the 32 docking protocols previously described for MVD (Xavier et al., 2016). 44

45 Docking Simulations-Molegro Virtual Docker Click on the OK button. 45

46 Docking Simulations-Molegro Virtual Docker You are one click to run MVD. On the new pop-up window, we can directly run any of the 32 docking protocols defined for MVD for the structure 1E1V, by clicking on any of the P# buttons (P01-P32). When we click on the Next button, SAnDReS takes you to the next structure on the Dataset directory. We can also define the number of runs and the number of poses created in each run. We will leave the default values. Click on the P01 button. 46

47 Docking Simulations-Molegro Virtual Docker SAnDReS automatically starts running MVD. You don t have to worry about the definition of the docking parameters for the Protocol 01, SAnDReS takes care of that for you. Just enjoy the ride... 47

48 Docking Simulations-Molegro Virtual Docker Once finished, we get the following message: Status: Finished. 48

49 Docking Simulations-Molegro Virtual Docker Click on the Close button on the MVD pop-up window. 49

50 Docking Simulations-Molegro Virtual Docker SAnDReS now carries out the statisical analysis of the docking results, as we have previously seen for AutoDock 4 and AutoDock Vina. Click on the Yes button. 50

51 Docking Simulations-Molegro Virtual Docker SAnDReS carries out statistical analysis of the docking results generated by the P01 of MVD... Once finished, SAnDReS can generate plots of the results. Click on the Yes button. We proceed as we have previously seen for AutoDock 4 and AutoDock Vina. 51

52 Docking Simulations-Molegro Virtual Docker Once finished, we could click on the P02 to carry out docking simulations using the Protocol 02. We are done here. Click on the Close button. 52

53 Docking Simulations-Molegro Virtual Docker Click on the Close button. 53

54 Import Docking Results SAnDReS can automatically read docking results generated from GemDock 2.1 (Yang & Chen,2004) and SwissDock (Grosdidier et al., 2011), besides the previously mentioned docking programs AutoDock 4 (Morris et al., 1998), AutoDock Vina (Trott & Olson, 2010), and Molegro Virtual Docker (Thomsen & Christensen, 2006) that SAnDReS natively run. To import docking results, click on Docking Hub- >Import Docking Results. 54

55 Import Docking Results On the new pop-up window, we may choose the docking program. In this tutorial, we have files for docking results generated from all five programs. Click on the AutoDock 4 button. 55

56 Import Docking Results We have previously run a docking simulation using AutoDock 4. The results for this docking simulation are on the docking.dlg file. SAnDReS is able to read this file and generate a CSV file with scoring function values and RMSD for all poses. The structure used for this docking simulation was 4ACM. We have prepared a tutorial about how to run AutoDock 4, you can access it clicking here. Click on the Generate CSV file button. 56

57 Import Docking Results If everything goes fine, we will see the docking results on the text GUI. 57

58 Import Docking Results SAnDReS has read the docking.dlg file to get the atomic coordinates for the poses and also the values for the terms of AutoDock scoring function. SAnDReS took the atomic coordinates in the lig.pdb file, as the crystallographic position and use them to calculate the RMSD values for each pose on the docking.dlg file. The results are stored in the redock01.csv shown below. 58

59 Import Docking Results Click on the Close button. 59

60 Import Docking Results Click on the Close button. 60

61 Import Docking Results We are now ready to analyze the docking results. Click on Docking Hub->Statistical Analysis of Scoring Functions vs RMSD. 61

62 Import Docking Results Click on the Yes button. 62

63 Import Docking Results SAnDReS carried out the analysis of docking results and generated the strmsd.csv and strmsd.log files with the results. The results are shown on the GUI and text windows. SAnDReS also generated a CSV file for each term in the scoring function. We have previously seen this task (strmsd.in). 63

64 Import Docking Results To generate scatter plots of scoring functions against RMSD, click on Docking Hub->Prepare Files to Plot Re-dock Results (Scatter Plot). 64

65 Import Docking Results The new pop-up window is the familiar interface to define the parameters to generate plots, previously discussed on this tutorial. Click on the Generate Files button, then click on the Close button. 65

66 Import Docking Results Click on Docking Hub- >Plot Re-dock Results (Scatter Plot). 66

67 Import Docking Results Click on the Plot pltcsv File button. We have already seen this interface working to generate plots. 67

68 Import Docking Results SAnDReS generated a new scatter plot. Click on the Close button. 68

69 Import Docking Results To import docking results from the other programs, we proceed in a similar way. Only keep in mind to have the docking results files generated by each docking program on the project directory. 69

70 Import Docking Results In the table below, we have the output files generated by each docking program necessary to carry out docking analysis by SAnDReS. Docking Program AutoDock 4 AutoDock Vina GemDock Molegro Virtual Docker SwissDock Files Necessary to Run SAnDReS docking.dlg and lig.pdb lig.pdbqt, lig_out.pdbqt, and lig.pdb lig.pdb and gemdock.xls DockingResults.mvdresults lig.pdb, lig.mol2, and clusters.dock4.pdb The lig.pdb file is not generated by any of the docking programs. This file is the crystallographic position for the ligand, and it is used as reference for RMSD calculation. 70