JADOPPT Version 1.0

(Tutorial)

(Java based Autodock Preparing and Processing Tool)

JADOPPT is a collaboration between the Universidad de Salamanca (Spain) and

the Instituto Politécnico Nacional (México)

November 2014

Note: JADOPPT is fully written in Java, and it is not necessary any extra API. The

applied molecular visualization is Jmol1, which is an efficient tool that consumes only

a small amount of resources. Jmol is bundled in JADOPPT.

Requirements:

Java 7 (JRE or JDK)2

4 GB in RAM (minimum).

Mouse (for a better handling of Jmol)

Windows XP, Vista, Win7 and Linux (Ubuntu, LinuxMint, and if possible

other flavors of Linux)

JADOPPT proved to have a better performance with Linux. Therefore, it is

recommended to use Linux.

The compressed file JADOPPT.rar contains the following files and folders:

JADOPPT.sh

JADOPPT.bat

dist

img

Settings

The files JADOPPT.sh and JADOPPT.bat execute the application, *.sh for Linux and *.bat

for Windows.

For Linux it is necessary to give a permission of execution, write the following instruction

in the terminal:

$chmod +x JADOPPT.sh

1 http://jmol.sourceforge.net/index.es.html 2 http://www.oracle.com/technetwork/java/javase/downloads/index.html

In graphic mode, use the mouse on the file and the right button, click on properties and then

on permission. Select the field: “execute file as a program”. For Windows it is not

necessary to give permissions.

To execute in Linux and Windows do double click on the file JADOPPT.sh or

JADOPPT.bat.

To increase the memory for the virtual machine, edit the files JADOPPT.sh or

JADOPPT.bat with a simple text editor (do not use Word in case of Windows).

Before:

java -client -Xms1000m –Xmx1300m -jar dist/TesisDoctoral.jar

After:

java -client -Xms2000m -Xmx8000m -jar dist/TesisDoctoral.jar

Step 1: Create a folder that contains the following files:

a) The results of the experiments of docking, dlg files (obligatory)

b) Map files (obligatory)

Create a folder that contains the protein or proteins:

c) Protein in PDB format (optional for analysis but recommendable to have)

Create a folder that contains a references or references:

d) Reference structures in PDB format (each reference in a separate file).

Step 2:

Select the folders that contain the files previously mentioned:

Step 3: Select a clustering method: RMSD or hierarchical

Step 4: Automatic selection of representatives (optional)

Step 5: Visualization results

Reference

files

Load dlg file folder

Working directory Distance method Dlg files

Map

files

Clustering

method RMSD

distance

Automatic selection of representatives

Protein file

Dlg menu files

Dlg files

a) Visualization for RMSD clustering

The clustering visualization with the RMSD method is displayed through a box-like

visualization and is linked with the Jmol display.

Binding energy color range

High affinity Low affinity Elements of the selected

cluster

Selected Cluster

b) Hierarchical clustering results:

The hierarchical clustering visualization is a dendrogram and is linked to the Jmol display.

Step 6: Clustering of the selected representatives

Clusters of the

current level Level cut bar

Observers to choose Clustering method

Selection of observer

based on the atom type

Selection of atoms group

Observer options:

a) All observers: use all file maps

b) Each atom:

c) Group Atoms:

a. C, A, N

b. OA, SA, NA

c. F, Cl, Br, I

d. HD

e. é

Step 7: Visual analysis of clustering from all representatives

Main

dendrogram

Clusters

Selected Cluster

Binding energy

color code

Target

Target cavity visualization

References

Jmol

Cluster elements

Cluster

elements

Zoom of the selected cluster

Other tools in JADOPPT:

In order to visualize the representatives of a specific dlg file: the menu in the

visualization window contains all the options from the representatives. The option

“Representatives from dlgs” highlights the representatives in the

dendrogram.

JADOPPT can reduce the number of elements through a re-filtering of the selected

representatives, with the option:

Dlg files

Selected representatives

from E7010B_3HKC.dlg

Distribution of the representatives from the E7010B_3HKC.dlg file

Using the initial data set

Using the current

visualized data

RMSD filtering new value

Binding energy filtering range

Filtering by the first best 5

Filtering by the first

best 5 clusters

In order to display the target cavity where the docking was performed and make the display

less loaded, the user can use the button which will display a new window with

the references, choosing one of them it will center on the cavity relative to the references,

hiding the rest of the protein.

Estructuras de referencias del análisis

Target cavity with the 02_COL_4c reference

Tools for Modifying MAP Files and Cloud Visualization

To visualize the map files used in the docking project the menu has two

options:

Visualize the clouds (Cloud Maps)

Create new clouds (New Surfaces)

Visualize the clouds (Cloud Maps):

Filtered values

from the map files

Grid points

References

Create new clouds (New Surfaces)

New group of

clouds

References

Map File to modify

Map File to

modify

Add new

cloud

Add new group

of clouds