myPresto GUI Free software

myPresto Portal
Ver.1.1.98

Quick manual

Japan Biological Informatics Consortium

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Table of Contents
1.

Removal of functional limitations ............................................................................. 32.

MD Calculations ........................................................................................................ 4
2.1.

Molecular Input .................................................................................................. 4

2.2.

Automatic MD calculation.................................................................................. 5

2.3.

Trajectory Analysis ............................................................................................. 7

2.3.1.

When MD calculation is performed in GROMACS ..................................... 7

2.3.2.

MD calculation by other than GROMACS .................................................. 8

2.4.
3.

Docking calculations .................................................................................................. 9
3.1.

Molecular Input .................................................................................................. 9

3.2.

Automatic docking .............................................................................................10

3.2.1.

Select receptor and ligand molecules .........................................................10

3.2.2.

Create a pocket ........................................................................................... 11

3.2.3.

Docking execution.......................................................................................13

3.3.
4.

5.

6.

3D Animation Display and File Output ............................................................. 8

Confirmation of Results.....................................................................................13

Saving and Loading Projects ....................................................................................14
4.1.

[File] - [Save As] ................................................................................................14

4.2.

[File] - [Open Project] ........................................................................................15

3D View of Molecular Structure ...............................................................................16
5.1.

Mouse Operation ...............................................................................................16

5.2.

Select molecule, chain, residue, atom ...............................................................16

5.3.

Select a display model .......................................................................................17

5.4.

How to color .......................................................................................................17

MD Calculations in GROMACS ...............................................................................18
6.1.

[Preference] - [Molecular dynamics] settings ....................................................18

6.1.1.

If [GROMACS] is selected ..........................................................................18

6.1.2.

If [Use chiral server=Yes] is selected..........................................................192

1. Removal of functional limitations
myPresto Portal is a limited version of MolDesk Basic with some limited functionality.
The restricted functions are as follows* The molecular weight of compounds (ligands) for which docking calculations can be
performed is limited to 400 Da.
* The total number of atoms in the system for MD calculations is limited to 25,000
atoms.
If you want to remove these limitations, please consider MolDesk Basic or MolDesk
Screening by IMSBIO Co., Ltd.
* IMSBIO Co., Ltd.

https://www.imsbio.co.jp/* MolDesk

https://www.moldesk.com/* MolDesk EC shop

https://moldesk.official.ec/

32. MD Calculations
For the Windows version, MD calculations (molecular dynamics calculations) withGROMACS can be performed with a few clicks of the mouse.
The following is an example of the simplest automated MD calculation.
The procedure is as follows.

2.1. Molecular Input
If you are connected to the Internet, click the [PDB] or [TEST]
button on the top page.
Each has the following functions.
[PDB]: Input the molecule of the PDB ID specified by the user.
[TEST]: Input molecules with any PDB ID 4kn6.
When the [PDB] button is clicked, thescreen shown in the figure is displayed,so enter 4kn6 and click [OK].

4kn6 will be entered.
The same applies when you click the[TEST] button.

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* If you are not connected to the Internet, click [File] - [Open Molecular File] to load thesample / PDB / 4KN6.pdb file.

2.2. Automatic MD calculation
Next, click the [MD] button shown in the figure.
The process is performed in the following order.
* Add missing hydrogen atoms to all molecules (default is the dissociated state in water)* Gasteiger charge added to all compounds or sugars* Molecules other than compounds or sugars are charged based on the force field
selected in [Help] - [Preference] - [Molecule] - [tplgeneX]

Displays a dialog box for
selecting water solventsand ion addition methods.
Click the [OK] button.
The water solvents and ionsare added.

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Solvent: A rectangular box with the center of gravity of the system as the center of thesolvent and a size of 3 Å from the solute boundary.
Ions:

Na+, K+, and Cl- are added at the ion concentration of a human cell.
Click [OK] to display the dialog box for setting
conditions for energy minimization
calculations.
Two energy minimization calculations will be
performed in succession.
The first one is the steepest descent methodwith 5000 steps. No position constraint
The second one is the conjugate gradientmethod, 5000 steps. No position constraint

When the energy minimization calculation is completed, the MD Calculation Condition
Setting dialog box is displayed.
Click the [OK] button.
The MD calculation starts withthe following conditions.
* Execute only once.
* The number of steps is 20000.
* NPT ensemble* Pressure is 1 bar.
* Initial temperature 300K
* Constant temperature of 300K
* No position constraint* Time step is 2.0 fsec
* Cutoff radius is 10.0 Å.
* Energy file output (every 2000
steps)* Trajectory file output (every
2000
steps)

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This completes the entire process of calculating MD for molecules in aqueous solution.
* The force field is set by default to AMBER GAFF2 for compounds or sugars and
AMBER ff99SB for others (e.g. proteins).
(Force field can be changed by [Help] - [Preference] - [Molecule] - [tplgeneX])* The [MD] button is equivalent to the[Dynamics] -[Auto Solvate andDynamics] button.
2.3. Trajectory Analysis
2.3.1. When MD calculation is performed in GROMACS
Click the [2D plot] button to run the trajectory analysis in GROMACS and display agraph with time axis linked to the movie.

gmx energy

gmx rms

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Executable gmx commands
GeneralPCA Analysis(1) gmx energy(8) gmx covar(2) gmx rms(9) gmx anaeig(3) gmx rmsf(4) gmx gyrate(5) gmx mindist(6) gmx hbond(7) gmx rama
* For details on usage, please refer to the MolDesk Basic manual.
* For details on trajectory analysis with GROAMCS, refer to the GROMACS manual.
2.3.2. MD calculation by other than GROMACS* For details on usage, refer to the MolDesk Basic manual.

2.4. 3D Animation Display and File Output
By operating the Animation controller on the MD
Analysis screen, you can animate the time variationof atom movement (trajectory) on the 3D screen.
Click the [Save Animation] button to output the
animation as a GIF file. The frame time interval canalso be set.
Click the [Save PDB] button to save a snapshot of all
trajectories in a PDB file.

83. Docking calculations
The following is an example of the simplest docking calculation performed byautomation.
The procedure is as follows.

* Docking to nucleic acid molecules in addition to proteins is available in ver. 1.1.78 andlater. Proteins or nucleic acid molecules can be specified as acceptors.

3.1. Molecular Input
If you are connected to the Internet, click the [PDB] or [TEST]
button on the top page.
Each has the following functions.
[PDB]: Input the molecule of the PDB ID specified by the user.
[TEST]: Input molecules with any PDB ID 4kn6.
When the [PDB] button is clicked, thescreen shown in the figure is displayed,so enter 4kn6 and click [OK].

4kn6 will be entered. The same applies when you click the [TEST] button.
* If you are not connected to the Internet, click [File] - [Open Molecular File] to load thesample / PDB / 4KN6.pdb file.

93.2. Automatic docking

Next, click the [DOCK] button in Fig.
The process is performed in the following order.
* Adds a missing hydrogen atom to all molecules (default is the dissociated state inwater).
* Add Gasteiger charge for all compounds or sugars* For molecules other than compounds or sugars, add charges based on the force field
selected in [Help] - [Preference] - [Molecule] - [tplgeneX]* The [DOCK] button is equivalent to[Dock] -[Auto Docking].

3.2.1. Select receptor and ligand molecules
A message dialog will appear prompting you to select a receptor.

Selectpro1 in the tree view screen and click OK.
The notation ofpro1 changes topro1 [Receptor]

because pro1 is recognized as a receptor.

* The receptor molecule must contain at least one protein or nucleic acid molecule.
It may contain compounds, sugars or metals.

103.2.2. Create a pocket
After specifying the receptor, a dialog box will appear to select the pocket creation
method.
In this case, leave [Make Pocket] as it is and click [OK].

The following is a description of the items in the dialog box for selecting the pocket
generation method.
Item

Item

[Coordinates of the ligand]

The coordinates of the selected molecule are used as the probe
point for the pocket.
Multiple molecules other than protein or nucleic acid molecules
can be selected and batch probed.

[Make Pocket]

Places a pocket sphere on the surface of the selected receptor
and generates a pocket probe point inside the sphere.

[Find Pocket]

Performs a pocket search on the surface of the selected receptor
and automatically generates multiple probe points in scoreorder.

* For details on usage, please refer to the MolDesk Basic Manual.
The protein becomes a space-fill display model and displays a pocket selection dialog.

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Click around the ligand molecule in the 3D screen.

The selected pocket is displayed
as a yellow translucent sphere.

Click the [OK] button.

Display

point4 in the tree view screen,

Add the probe points (red points) of the pocket in theyellow translucent sphere.

A message dialog prompting the user to select a ligand is displayed.
In this example,

lig2 is selected in the tree

view screen and [OK] is clicked.

123.2.3. Docking execution
A dialog box for setting the conditions for docking calculations appears.
In this example, leave the default conditions as
they are and click OK. The docking calculation is
executed.
All docking calculations are now complete.

3.3. Confirmation of Results
When the docking calculation is completed, the Docking Info screen displays a list of the
10 molecular structures predicted by the docking calculation in order of best score.
The values of the molecular structure attributes are as follows
ΔG value (deltaG, free energy)
Score (score, docking score)
RMSD (value for the ligand used in the docking calculation input)
Clicking on amolecule in theDocking Info
screen andclicking the ↑↓keys will display
the selected
molecule one by
one in the 3D
screen.

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Select a candidate structure in the Docking
Info screen (Ctrl+click for multiple selections),right-click, and select "Add Selected Docking
Result" to add the candidate structure to the
Ligand Info screen, Add Selected Docking
Result" to add the candidate structure to the
Ligand Info screen. The result will be added to the calculation system and can be used
for MD calculations, etc.

4. Saving and Loading Projects
4.1. [File] - [Save As]
Saves the displayed system with a project name. The command history is also saved.
Execute [File] - [Save As] and in the [Make PROJECT directory] dialog,
select [Create New Folder] or [New Folder]or [New] - [Folder] from the right-click menu
and enter a folder name. This folder name will become the new project name.
All data (including command history) of the currently displayed system will be saved in
the created folder.
[Please note that if you specify an existing folder without creating a new folder, thefollowing folders and files will be output directly under the folder.
original folder
work folder
cif and pdb files downloaded via internet* If you are interested in the details of the files stored in the project, please refer to the
MolDesk Basic Manual.

144.2. [File] - [Open Project]Open a project that has been saved in the past via [File] - [Save As],or
MoldeskProject00000
MoldeskProject00001
MoldeskProject00002…
in the directory set in the Default Project Directory under[Help] - [Preferences] - [8. Other].
Select the existing project folder (including “original” and “work” folders directly below)
and click [OK].
The tab names on the tree display screen (blue box "P2- L1- W" in the figure below)
indicate the number of proteins and compounds.
P indicates protein chain, L indicates compounds, W indicates the presence of crystal
water, and M indicates metals and ions.
In the tree view,

denotes protein,denotes metal ion, anddenotes compound,denotes water,

denotes sugar.

The last command is indicated by the tab name on the 3D screen ("proj001 : 5 Global
Minimize" in the red frame in the figure below).
The tab name indicates [Project name : History number Execution command name].

Executed commands can be confirmed by clicking

15[UNDO] or[REDO].

5. 3D View of Molecular Structure
5.1. Mouse Operation
Rotate and move molecules on the 3D screen with the mouse.
Movement

Mouse Operation

X-axis (left/right axis) rotation

Left dragY-axis (vertical axis) rotation
Z-axis (depth axis) rotation

Shift + right drag (left/right direction)

Move in X-axis (left/right) direction

Right dragMove in Y-axis (up/down) direction
Move in Z-axis (depth) direction (zoom in/out)

Shift + left dragOr, rotate the wheel* For MAC, Left click = click
Right click = [Command] + click

5.2. Select molecule, chain, residue, atom
The selection of molecules, chains, residues, and atoms is performed with the mouse,but the operation differs between the 3D screen and the tree view screen.
Operation

3D Screen

Tree view screen

Multiple selection

Ctrl + click

Ctrl + click-

Shift + click

Select residues

Double click

Click residue name

Select Chain

Triple click

Click on chain name

Select molecule-

Click on molecule name

Consecutive
multiple selections

Multiple molecules, chains, residues, and atoms canbe displayed or hidden together.
Select multiple molecules, chains, residues, andatoms in the tree view and right-click [Show Atom]or [Hide Atom].
Click [Show All] to show all residues and atoms.
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5.3. Select a display model
By selecting a molecule, chain, residue, or atom,and then selecting a model from the [Display]
menu, you can change the display model to Line,
Stick, etc.
The meaning of the options are as follows[Only] : Display only this display model in 3D.
[On] : Overlays this display model on otherdisplay models.
[Off]:

Erase this display model.

For other display models, please refer to the following site of MolDesk
https://www.moldesk.com/moldesk-basic-commands/#Display

5.4. How to color
You can change the color of molecules, chains, residues, and atoms.
Select a molecule, chain, residue, oratom, and choose a color from the[Color] menu to change its color.
You can also change the color andtransparency of all molecularsurfaces at the same time by
selecting [Color] - [All Surface].
For more information on each item in the [Color] menu, please refer to the following siteof MolDesk.
https://www.moldesk.com/moldesk-basic-commands/#Color17

6. MD Calculations in GROMACS
6.1. [Preference] - [Molecular dynamics] settings
6.1.1. If [GROMACS] is selected
In the [Help]-[Preference]-[Molecular dynamics] screen, select [GROMACS] under[Molecular Dynamic Program : ].
Performs energy minimization and MD calculations with GROMACS on a computerwith MolDesk Basic installed.

On Windows 10 and Windows 11, this setting is not necessary since the GROMACS
executable program is implemented beforehand.
On Linux and MAC, the user must install GROMACS and configure the [GROMACS
directory] setting in the installed GROAMCS. The installation procedure is explained
below.
https://www.moldesk.com/faq/faq16/
For [GROMACS directory], set the directory where share and bin exist.
* In the current version, GROMACS is executed in bin/gmx without specifying thenumber of parallelism.
If bin/gmx does not exist in the installation directory, GROMACS cannot be executed.

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The parallel number of OpenMP and thread MPI depends on the function of
automatically specifying the parallel number of GROMACS.

6.1.2. If [Use chiral server=Yes] is selected
When Yes is selected for [Use chiral server :] in the [Help]-[Preference]-[Molecular
dynamics] screen

The energy minimization and MD calculations are performed by GROMACS on thecloud server provided by Chiral. A separate contract between the user and Chiral isrequired.
Enter the [Chiral Server User ID] and [Chiral Server API Key] issued by Chiral.

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