Using Autoscreen


Lesson 1: Analyzing 2D 15N-HSQC spectra of calcyclin

This lesson presents the basic steps of SAR by NMR analysis using the Autoscreen module of FELIX. In this lesson you use a set of three 15N-enriched HSQC ser files of calcyclin acquired on a Bruker spectrometer and some PDB, CAR, and MDL files.

The topics covered in this lesson are:

1.   Setting up for the lesson

All the files in the $BIOSYM/tutorial/felix/sar directory are required for this lesson.

To copy all files in the sar directory to your working directory, go to your working directory and enter at the UNIX prompt:

It is important to use this command so that you retain the relative paths for these files.

The files are briefly described below:

The mols.txt file is a list of structural files, with each line specifying the structural file for one molecule, as follows:

     demo.pdb
test.car
test2.mol

The exps.txt file is a list of input experiments and their associated structural files, with each line specifying the experiment ID, ser file (with path relative to /usr/people/cpeng/sarnmr/test/scripps/; see Step 3 for project paths), file type, structural filename (optional), and comments (optional):

     calcyclin	1/ser	ser	demo	control
annexinXI_34 2/ser ser test.car test-1
annexinXI_48 3/ser ser mols.txt

2.   Starting FELIX

In your working directory, enter this UNIX command to go to the directory for saving the analysis results:

Then enter this UNIX command to start the program:

If you get the RESTORE LAST SESSION dialog box, select CANCEL.

Select File/Open and set the File Type to DBA. Specify example for the file name and select OK to build a new database.

Note: If you set up an Autoscreen project in the previous session and want to use the same spectrum display and scoring parameters as in that project, select OK in the RESTORE LAST SESSION dialog box. Spectrum-processing parameters are not inherited from session to session.

3.   Setting up the project

Select the Autoscreen/Project menu item from the FELIX menu bar. When you see the AUTOSCREEN PROJECT control panel, leave the default Project Name unchanged (sar) and select OK.

You should see this in the text window:

     Created new Autoscreen project 'sar'.
Note: Currently a project name is limited to less than nine lower-case alphanumeric characters. You can create only one Autoscreen project in a database. Once a project is finished, you can select the File/New menu item to open a new database after saving the current one, and then repeat this step to create a new project.

The VERIFY DIRECTORIES control panel, which appears next, allows you to verify some important paths used to access or save the following files:

For this example, you are using relative paths for all experiments and molecular files, so it is important to verify the project paths.

Make sure that the paths in the VERIFY DIRECTORIES control panel are similar to the following:

Data: /usr2/people/cpeng/sar/
Matrices: /usr2/people/cpeng/sar/analysis/
Molecules: /usr2/people/cpeng/sar/str/
ASCII Files: /usr2/people/cpeng/sar/analysis/

You can click Browse next to any of the paths to select a directory interactively or you can directly enter a directory name.

Select OK.

This displays an empty Autoscreen Experiments Table.

Note: If you want to change the project paths again, use the Edit/Verify Directories menu item in the table or the Autoscreen/Experiment/Verify Directories item on the main menu bar.

4.   Adding experiments to a project

The following steps demonstrate three ways of adding experiments to an Autoscreen project.

Option 1 - Add one experiment at a time

Select the Autoscreen/Experiment/Add One menu item.

In the ADD ONE EXPERIMENT control panel, select Bruker (ser) as the Spectrum File Type, enter Control as the Experiment ID, and fill in the Comment with This is the control experiment.

If you want, you may turn on the Molecule toggle and click the Browse button. When the SELECT MOLECULAR FILE OR FILE LIST file browser appears, select demo.pdb and select OK to return to the ADD ONE EXPERIMENT control panel.

Finally, select the ser file under the directory sar/1/, and select OK to add this experiment to the project.

The Autoscreen Experiments Table is updated with the newly added experiment.

The ADD ONE EXPERIMENT control panel is displayed again for you to add another experiment. Select Cancel if you are finished.

Note: If you select a molecule file interactively, be sure to do so before selecting the ser file. Otherwise, FELIX does not "remember" that you selected the ser file and you will have to do it again.

Option 2 - Add experiments from all files in a directory

First clean up from your test of the previous option:

Highlight the row of interest (or all rows if you added more than one experiment) in the Autoscreen Experiments Table and select the Edit/Delete Experiments menu item to remove the experiment.

Next, add experiments from all files:

Select Autoscreen/ Experiment/Add All Files. In the ADD ALL EXPERIMENTS control panel, change To Dir to 3, the highest experiment number. Then select OK.

All three experiments are added to the project, with the first experiment taken as the control spectrum.

Note: This function expects numbered Bruker experiments. If the experiments are not consecutively numbered, you can instruct the program to skip one or more between every two experiments, or it will automatically ignore nonexistent experiments.

Option 3 - Add all experiments listed in a file

First clean up from your test of the previous option:

Highlight all rows in the Autoscreen Experiments Table. From the table, select the Edit/Delete Experiments menu item to remove all the experiments.

Next, add experiments by reading a list in a file:

Select the Autoscreen/ Experiment/Add From File List menu item and, in the ADD EXPERIMENTS FROM FILE LIST control panel, select the file exps.txt and select OK.

This adds three experiments to the project, using the experiment list in the exps.txt file. These experiments are the ones that we will use in subsequent processing and scoring in this lesson.

5.   Processing a control spectrum

Unless you are using processed data, for example, FELIX matrices or Bruker 2rr files, one of the most important steps in using Autoscreen is processing the control spectrum. The processing parameters used during this procedure are used for the subsequent processing of all other test experiments.

Highlight the calcyclin experiment in the Autoscreen Experiments Table and select Action/Process Control Spectrum from the menu bar of the table.

Next you are guided through the processing of this 2D experiment. The procedure is similar to standard 2D processing in FELIX.

Keep the default parameters unchanged and select OK in the 2D HEADER INFORMATION and 2D ACQUISITION INFORMATION control panels.

In the 2D DATA PROCESSING control panel, which appears next, select Automatic for Phasing Mode and Facelift for Baseline Correction. Select OK.

You will use the automatic phasing function (called PAMPAS) and baseline-correction function (called FACELIFT) after the Fourier transform.

Note: PAMPAS automatically determines phasing parameters for a processed matrix. You will be prompted to set parameters for it later. If you want to phase interactively, select Interactive as the Phase Mode and enter 3 for Fid to Phase.

Select OK in the SINEBELL PARAMETERS control panel. If it warns you about overwriting an existing file, click Overwrite.

In the 2D DATA PROCESSING control panel, check Linear Prediction, select Automatic as the Phasing Mode, and Facelift as the Baseline Correction. Select OK.

In the GENERAL LINEAR PREDICATION control panel, change the Number of Coefficients to 8 and select OK.

Select OK in the SINEBELL PARAMETERS control panel.

In the AUTOPHASING (PAMPAS) PARAMETERS control panel, check Correct D1 and Correct D2. Under Excluded Areas, check #1. Click the Cursor button on the same line to set the excluded area interactively.

The purpose of this action is to exclude the water signals while determining the phase parameters. The cursor changes to a cross, allowing you to define a range to exclude for D1

.

Click at a point between the real peaks and the water signals, keep the left mouse button depressed, and drag the cursor to the right limit of the spectrum (the Y coordinates do not matter), then release the mouse button.

The same control panel appears again with the excluded range displayed in points (for example from 374 to 512). If necessary, you can edit these numbers in the entry boxes.

Select OK.

The spectrum is automatically phased in both dimensions. In the text window, the determined phase parameters and other information are displayed.

Note:  

Finally, the BASELINE CORRECTION (FACELIFT) PARAMETERS control panel appears. Make sure D1 and D2 are checked for Correction Dimension and select OK.

The processed HSQC spectrum is now displayed as contours.

6.   Setting display reference and display limits

The reference, display limits, and threshold are set using the general FELIX menu items or icons.

Select Preference/Reference. In the REFERENCE MATRIX control panel, set these parameters:

Reference Point
D1: 462
D2: 64

Reference Shift
D1: 4.7
D2: 117.99

Axis Text
D1: D1_H1
D2: D2_N15

Select OK.

Use the Zoom icon on the FELIX tool bar to zoom in on the fingerprint area.

Select Preference/Plot Parameters. In the PLOT PARAMETERS-BASIC control panel, enter 0.025 as the Contour Threshold. Select OK.

Finally, select Autoscreen/Save Limits and Reference to save the reference, limits, and threshold.

These parameters will be used for display, hardcopy, and scoring of all experiments in the project.

Note:
Note: If you make any changes to these parameters, be sure to use Autoscreen/Save Limits and Reference to save them -  otherwise the changes are lost. You can change the display limits and threshold at any time (for example, after processing and scoring some test spectra), but the reference must be set before you select Autoscreen/Setup Scoring to define scoring parameters.

7.   Setting other display parameters

Many other display parameters can be changed and saved along with the project by selecting Autoscreen/Setup Display. These include the display parameters for the control spectrum and test spectra in contour mode and overlay mode and those for display of control peaks. For this lesson the default values are used.

Note:  

8.   Picking peaks and importing an assignment for the control spectrum

In the Autoscreen Experiments Table, double-click the Control spectrum to display it.

Select Peaks/Pick Region from the main menu and use the default parameters to pick all the fingerprint peaks.

About 82 peaks are picked and displayed in the Peaks-xpk:peaks table.

Note:  

Select the Autoscreen/Import Assignments menu item. In the IMPORT ASSIGNMENTS control panel, select BMBR Assignment Table as the Assignment File Type and select the file bmrb_assign.tbl from the browser.

Select OK.

The text window reports that 17 peaks have been assigned. The assignments are also updated in the Peaks-xpk:peaks table.

To display the assignments on the spectrum, select Autoscreen/Setup Display, select Residue for Peak Labels, and select OK.

Note: The bmrb_assign.tbl file is not a real or complete file and should only be used for demonstration purposes.

9.   Setup of scoring parameters

In this step you set up parameters for peak picking in and scoring of test spectra.

Select Autoscreen/Setup Scoring. In the 2D SCORING PARAMETERS control panel, click the Advanced button to review parameters in the ADVANCED PARAMETERS FOR 2D SCORING control panel. Leave the default values unchanged and click Cancel to return to the 2D SCORING PARAMETERS control panel. Leave its default values unchanged and select OK.

Note: The following briefly explains the parameters for scoring:

Basic parameters (in 2D SCORING PARAMETERS control panel):

Advanced parameters in ADVANCED PARAMETERS FOR 2D SCORING control panel:

All other parameters in this section are the same as for standard 2D peak picking. The same values as for the control spectrum are recommended for them.

The toggles Use Peak Widths and Use Peak Heights, if checked, allow the shape of peaks to be considered.
If peak shape is used, Minimum Shape Similarity is a threshold for two peaks to match.
Search Methods provides two alternative algorithms to search a best match between the test and control peaks. If Tree Search (the default) is selected, a heuristic depth-first search method is applied. Since this can be time-consuming, you can limit the CPU time spent on each test spectrum by defining a value for CPU Time Limits (default = 10 s). If Simulated Annealing is selected, the stochastic method is applied. The latter is usually fast (so CPU Time Limits is not used), yet does not guarantee a best match. The latter method is recommended when the spectra are so complicated that tree searching does not give satisfactory results in a reasonable amount of CPU time.

For each unmatched control peak, if Fit to Test is selected, it will be fitted to the test spectrum using the peak optimization function if the percentage of unmatched control peaks has not exceeded the Maximum (%). (For details see Peaks/Optimize (page -200) in Chapter 4, Processing, visualization, and analysis interface (1D/2D/ND) in the FELIX User Guide.) If the fitting is successful, the optimized peak is taken as its matched test peak. Otherwise it remains unmatched, and a Penalty (default 0.60) contributes to the score of the experiment.
For unmatched test peaks, Selection allows you to select the method to define them. If None is selected, such peaks are ignored. If Close to Control Peaks is selected, only those that are close to at least one control peak, namely with displacements not bigger than the Maximum D1 (or D2) Peak Displacement Limits, are included. Otherwise, if All is selected, all peaks are included. When determining if it is a legitimate test peak, FELIX compares the peak widths and height of a test peak with the statistics of all the matching test peaks. The parameter Num.of RMSD (default 2.0) then allows you to define a tolerable deviation from the average peak widths and height. Finally, the Penalty is the contribution of each unmatched test peak to the score of the experiment. The default (0.2) is smaller than for an unmatched control peak (0.6), because automatic picking of test peaks is usually less reliable than picking of control peaks, which is normally done manually where refinement is possible.

A Peak Displacement Table is displayed. The table contains the following columns:

Note:  

10.   Processing and scoring test spectra

Once you have set up the scoring parameters, you can process and score all the test spectra.

Select Autoscreen/Go from the Autoscreen Experiments Table.

The two test spectra are processed and scored against the control spectrum in turn, then a histogram of scores vs. experiments is displayed. The Autoscreen Experiments Table is updated with the scores and status of the test experiments.

Note:  

Experiment annexinXI_34 shows a higher score than the other experiment, which usually indicates a stronger binding of the ligand to the protein.

There are five methods for processing and/or scoring test spectra on the Action menu in the Autoscreen Experiments Table, which are used for different purposes:

Note: The Peak Displacement Table is not updated at this moment. To display and update it for a certain spectrum, double-click it in the Autoscreen Experiments Table.

11.   Viewing clusters

Using the Autoscreen/View Clusters menu item groups experiments that share common displaced peaks, providing a way to locate the residues of the protein whose chemical shifts were affected by the close contacts of the ligand in different experiments.

Select Autoscreen/View Cluster, leave the default value of Cluster Threshold unchanged, and select OK.

The score matrix is displayed showing one cluster in green.

Move the crosshair cursor over the green area to display the peak number, experiment name, and contribution of that peak to that experiment. Press <Esc> when you are done.

Note:  

12.   Analyzing the scoring results

Once you have an overview of all experiments, you can investigate the interesting experiments and interesting peaks.

First highlight Experiment annexinXI_34 (the one with the highest score) in the Autoscreen Experiments Table and click the Peak Contribution Histogram icon. Leave the default values in the PEAK CONTRIBUTION HISTOGRAM OPTIONS control panel and select OK.

A histogram of contributions vs. peaks for this experiment is displayed. The Peak Displacement Table is updated with the scoring data for Experiment annexinXI_34.

To view the peak displacements, double-click Experiment annexinXI_34 in the Autoscreen Experiments Table.

The overlay contours of Experiment annexinXI_34 over the control spectrum are displayed, together with the displacement arrows and control peak labels. The scoring results are also summarized in the text window.

To get a clearer view of the displacement arrows, you can:

In the Autoscreen Experiments Table, click the Peak Contribution Histogram icon again to display the histogram of contributions vs. peaks of Experiment annexinXI_34.

Peak 73 has the largest contribution and seems to be an interesting peak.

On the Peak Displacement Table, click the Sort Contributions icon.

The peaks are now listed in descending order of their contributions to the score.

Highlight the first row, Peak 73, and click the Zoom on Peaks icon or simply double-click the row of peak #73.

The display zooms in on the displacement between control peak 73 and its matching test peak.

To display the titration of Peak 73, that is, its contributions in different experiments, highlight this peak in the Peak Displacement Table and click the Titration icon.

A histogram of contribution vs. experiments is displayed. This also shows that this peak has a much greater displacement in Experiment annexinXI_34 than in the other experiment.

13.   Manually editing scoring results

In the Autoscreen Experiments Table, highlight Experiment annexinXI_34 and click the Overlay icon.

Experiment annexinXI_34 is displayed over the Control spectrum together with the displacement arrows.

Click the Undo Sort Contributions icon in the Peak Displacement Table, then double-click peak 7 in the Peak Displacement Table to zoom in on the spectral area around it.

All control peaks appear to be correctly matched to the test peaks, so manually editing is not needed in this experiment. For demonstration purposes, the following operations assume that you do not like the currently matched test peads for control peaks 7 and 9 and want to change them.

To remove the current matching, select Edit/Remove Displacement from the Peak Displacement Table and click control peaks 7 and 8.

This erases the displacement arrows.

Press <Esc> to exit this mode.

Now select Edit/Change Displacement from the Peak Displacement Table and click control peak 7.

Keep the mouse button depressed and drag the cursor to the center of the test peak at (7.30,124.23) and release the button.

Repeat this for control peak 8 so that it is matched with the shoulder peak centered around (7.27, 124.46).

Press <Esc> to exit this mode.

This matches peaks 7 and 8 to the desired test peaks. All the changes you've made are reported in the text window and updated in the Peak Displacement Table.

Note:  

14.   Exporting scoring results

Select Autoscreen/Export Score. In the EXPORT SCORES control panel, set Contents to All Scores and Delimiter to Tab or Space. Enter the filename Test2 under Selection (a .dat suffix will be added automatically).

Select OK.

All the experiments and their scores are listed in the Test2.dat file.

Repeat the previous box with Contents set to All Scores Sorted.

This lists all experiments and scores in descending order.

Repeat the first box of this step with Contents set to Scores and Titration, Number of Experiments set to 2, and Number of Peaks set to 10.

The scores of the top two experiments, in descending order of scores, and the contributions of the top 10 peaks that have the greatest sum of contributions to the two experiments are reported.

Note: This function is intended to give a summary of the "interesting peaks in the interesting experiments." You can choose the numbers of experiments and peaks to report.

<Shift>-click to select the two test experiments in the Autoscreen Experiments Table and <Ctrl>-click to select peaks 60, 63, and 73 in the Peak Displacements Table. Then repeat the first box of this step with Contents set to Titration Selected, Delimiter set to Tab, and Use Comments as Concentration toggled off.

The contributions of the selected peaks in the selected experiments are reported. Such a report is intended for calculation of Kd based on titration. If you have specified the concentration of the experiments in the comment column in the Autoscreen Experiments Table, you can toggle on Use Comments as Concentration to include that information in the report.

Repeat the first box of this step with Contents set to C2 QSAR Table.

All experiments and scores are listed in a format suited for QSAR study with the Cerius2 program.

To import Autoscreen results into Cerius2 for QSAR study, take the following steps:

1.   Start Cerius2. Select the QSAR deck and click the Show Study Table item on the QSAR card. This brings up a new, empty QSAR Study Table.

2.   In the QSAR Study Table, select File/Import... In the Import/Table control panel, uncheck File Contains Row labels, check File Contains Column Labels, select the filename from the list box, and click Import. The experiments and score are displayed in the Table Manager.

15.   Scoring again with ROIs (regions of interest)

After getting an overview of all peaks in all experiments, you may want to focus on some interesting peaks in some interesting spectra instead of looking at all of them. When setting up the scoring parameters (see Step 9), all peaks in the Peaks-xpk:peaks table are taken as ROI peaks with weight equal to 1.0 by default. The following boxes demonstrate some of the methods for defining a subset of the peaks as ROI peaks.

Highlight the calcyclin spectrum in the Autoscreen Experiments Table and click the Draw icon to display it.

If the peak labels and peak numbers are not displayed, select Autoscreen/Setup Display and choose Small Cross for Crosspeak Symbol and Number # for Peak Labels.

Select OK.

Select Autoscreen/Define Region of Interest and click the tear-off line on the pullright menu. Move the Define Region of Interest menu to a convenient place on your screen.

Select Remove All.

This sets all peaks as nonROI peaks with weight equal to 0. Note the change of their color in the spectrum window.

Select Add Region. Drag out a rectangle around the peaks with H1 chemical shift greater than 9.0 ppm.

Note the change of color of these peaks and the report in the text window:

     Displaying 9 ROI peaks. Total 82 peaks.

In the Peak Displacement Table only these ROI peaks have non-zero weights.

Select Add One Peak. Click Peaks 1-5 and 73. Then press <Esc> to quit.

You have now about 15 ROI peaks. See the text window again for the number of ROI peaks.

After defining ROI, you can rescore the spectra you are interested in. Highlight Experiment annexinXI_34 in the Autoscreen Experiment Table and select Action/Score Selected Spectra.

Its score is reduced to 2.285. Only the ROI peaks, displayed in yellow by default, show displacement arrows in the spectrum window. Both the Peak Displacement Table and the text window show the scoring contributions of the ROI peaks only.

Click the Peak Contribution Histogram icon with Experiment annexinXI_34 still highlighted, to see the histogram of the contributions of the ROI peaks. You can select either Peak IDs or Residue Numbers as the x coordinates.

To score all experiments based on the newly defined ROI peaks, select Action/Re-score All Spectra and select OK in the control panel.

Note:  

16.   Printing spectra and histograms

To set up for printing, select Autoscreen/Setup Print. In the HARDCOPY PARAMETERS control panel, select Redraw Overlay as Plot Selection and PostScript as the Plot Device. Check Print Parameters and Send to Printer. Enter a UNIX command as the Print Command (for example, lpr -Pprintername).

Select OK.

In the Autoscreen Experiments Table, highlight Experiment annexinXI_34 and click the Print icon.

The text window reports the printing command it issues. You should receive a hardcopy of the overlay of annexinXI_34 over the Control spectrum, along with the displacement arrows and spectrum title and parameters.

Note:  

17.   Displaying molecules and scores in Insight II

As described in Step 1, some experiments are associated with a molecule file for demo purposes.

To display experiments associated with a molecule, first start Insight II from another UNIX shell window and go to the NMR_Refine module.

In the Autoscreen Experiments Table, highlight the calcyclin experiment and then click the Display Molecule icon to display the demo molecule.

Highlight the annexinXI_34 experiment in the Autoscreen Experiments Table. Select Action/Color Scores from the table.

In the COLOR RESIDUES BASED ON SCORE control panel, select InsightII as the Format and enter color as the filename.

Four assigned peaks with non-zero contributions are exported into file color.tab.

In Insight II, select Session/Change_Directory to move to the directory sar/analysis.

Select Query/Color_By_SAR_Score. In the control panel, set these parameters:

Sar_Molecular_Name DEMO
SAR_Score_Filename color.tab
Neutral_Color white
Num_Intervals 10
Low_Score 0.02
High_Score 0.2

Select Execute.

Note: If you are using Insight II version 980 or older, in which the Query/Color_by_Sar_Score command is not available, you can select File/Source_File to open the color_by_score.bcl script file to set up this command. The script file resides in the sar directory.

Wait until the rendering of the Connolly solid surface is complete. The residues that contribute to scores (between 0.02 and 0.2) are displayed in red.

18.   Exiting FELIX

To exit FELIX, select File/Exit.

Note: