SeeSAR 7.1 Beginners Guide. June 2017
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- Jeffery Chambers
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1 SeeSAR 7.1 Beginners Guide June 2017
2 Part 1: Basics 1
3 Type a pdb code and press return or Load your own protein or already existing project, or Just load molecules To begin, let s type 2zff and download it from the pdb! 2
4 The protein is loaded and protein ligands are listed in the table all fully automatic. Table - drag right rim to re-size - click entries to select Select a protein in the table on top to see the bound ligands. Optionally unfold some protein information here. 3D-viewer: - right-click to rotate - mouse-wheel to zoom - middle-click to shift 3
5 If you want to customize the layout of SeeSAR, click on the appearance button in the top right toolbar. Adjust background color Change the table layout Switch between dark and light theme Adjust label size Switch to color blindness mode For this guide everything stays on default, but please feel free to change it! 4
6 Note that there are two tabs. In the proteins tab you find all proteins and bound ligands. Note that each of these has it s own binding site (click on a ligand to see it in atomic detail). The molecules tab is to further work with any set of molecules in a common binding site. To transfer a protein ligand to the molecules table click on the menu button first and the molecule copy button second. 5
7 Note: working with the molecules table requires the definition of a common binding site. To do so, click on the define binding site button. 6
8 The define binding site dialog opens replacing the main menu! 1. Select a protein for binding site definition from the drop-down menu. 2. Use/select a molecule from the table to define the binding site or determine unoccupied pockets. For now, let s do the former and leave the dialog. 3. Upon selection the binding site appears in pink in the 3D window. Now leave the dialog via the green exit button and confirm your choice of binding site with the checkmark! Note: this brings you back to the main menu 7
9 The molecules table offers a lot of options: - on top you find general functions with an effect on multiple molecules in the table which you can select with the checkbox in the first column. - the selected molecule provides further functions (accessible through its menu button) To estimate the binding affinity click the thumbs-up button! Next, let s inspect the binding mode in detail. Zoom in using the space key on the keyboard! 8
10 As the 3D view easily gets busy, let s customize the visualization. 9
11 The view controls let you toggle on/off: Protein components Torsion coloring Surface Hyde coronas Unoccupied space Binding Site A click on the button toggles the visibility. Via the small triangles you may access more options. Let s hide the secondary structure, ligands, and metal ions as shown! Note: a click on the checkmark toggles the visibility of individual components. Clicking on header toggles the visibility of all components in the column/row (useful with several proteins). 10
12 The colored coronas depict the contributions of each atom to the estimated binding affinity. Red means unfavorable contribution, green a favorable contribution and the bigger the sphere is, the stronger is the effect. No sphere means that such atom is not estimated to have a significant impact on the binding affinity. To access the moleculespecific functions now, click on the menu button! 11
13 For a selected molecule you can: select mark as favorite annotate calculate affinity generate poses edit ligand delete toggle permanent visibility We want to edit the molecule so click on the edit button! This will open the editor menu at the top, again replacing the main menu. 12
14 The editor-menu lets you: add atoms or rings change charge adjust torsion remove atoms store the current molecule to the table change atom type change bond type ReCore parts of molecule undo/ redo exit the editor To edit a molecule ALWAYS: 1. select (atoms or bonds) 2. modify (using the function of choice from above) Note that many editor functions have shortcut-keys. E.g. select a bond and type 1, 2 or, 3 on the keyboard, or select an atom and type the element (C, N, O, ). 13
15 As an exercise, we add an amino group to the ring by selecting the Hydrogen in meta-position and changing its element type to N. Note: during editing you see all Hydrogens but no estimated affinity and no coronas. To see them, 1 st add the edited ligand to the table (with or without generation of poses), 2 nd select the new entry in the table and 3 rd calculate the affinity with the thumbs-up button! 14
16 If you click on the molecule entry you see the estimated affinity and related coronas, but only polar Hydrogens. The editor menu is locked now. To continue editing, click on the Resume button on top! 15
17 Now lets add a methyl group to the 5-membered ring. Again storing this in the table, we see a further increased affinity estimate. Let s leave the editor now by clicking on the exit button, keeping all edits with the checkmark. 16
18 At the top of the molecule table, you find the following options that act on multiple molecules in the table: define new binding site generate poses save molecules permanent visibility send to StarDrop toggle table/ grid view optimize & calculate Hyde edit molecules delete molecules filter molecules Hyde performance assessment 17
19 For report-preparation, you find the option to take a screenshot under the utilities button in the upper right toolbar: center view take screenshot For binding mode analysis, you find some useful mouse modes under the next button to the right: add labels measure distances measure angle measure torsion delete labels 18
20 Part 2: Adding own molecules 19
21 If you want to add your own molecules to a SeeSAR-session: use e.g. your favorite drawing tool and save the molecules as sdf-, smiles-, or mol2-file. Then load them in SeeSAR. In the source column you see where a molecule came from. 20
22 Loaded molecules may not yet be placed in the binding site (the information icon tells you upon mouse-over). In such case, select the molecules and use the Generate Poses button! (Note: obviously you can skip this step if your molecules are already placed in the binding site, e.g. by an external docking). 21
23 At most 10 poses per molecule are generate this way. To get the estimated affinities, press the thumbs-up button at the top of the table! Note: you may restrict the Hyde-calculation to a pre-selected set of checked molecules. 22
24 1 2 Now the estimated affinities appear as a range on the logarithmic (!) scale. To inspect multiple poses in comparison, toggle the permanent visibility with a click on the eye button (1.). Now it will appear in purple color and stay visible as you select other molecules. You can add more physico-chemical and ADME-properties as well as pharmacological parameters to your table with a click on the table button (2.). 23
25 By now you have a lot of interesting values and possibly many molecules. You may want to apply some filters Clicking on the filter button at the top opens the filter panel on the right side of the table. 24
26 To add a filter, select/determine a property from the dropdown list and push the Apply filters button (or simply hit return). For a better overview, slide the last filter element to the on position and see (from all those passing the filters) only the best-scoring pose per molecule. To hide the filter dialog push the filter button again. Note that filters may still be active then! 25
27 Part 3: Adding more proteins 26
28 Let s load in addition 2zda from the PDB. 27
29 Now you have 2 proteins in the protein table. As before, the protein ligands of the selected protein are listed underneath. In the binding site you see now the amino acids from both proteins. The selected protein appears a little brighter. To better discriminate between the proteins let s change the color in the protein table 28
30 This protein was used to determine the common binding site. To select a custom color, click on the rectangle in the second column! Different proteinrelated functions are accessible via the menu button. You may reset it with a click in the x. 29
31 Open the visualization dialog and toggle the visibility (of ribbons, binding site, ligands, water, and metals) for all (with a click on the column/row header) or individual components! 30
32 This has been a lot At any time find help within SeeSAR here! 31
33 Now we wish you happy SeeSAR-ing! 32
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