chapter 1 system tutorial and manual

Chapter 1

System Tutorial and Manual

This appendix present a short manual for exploiting the package as fast as

possible.

Preliminary steps:

� Download and install all the applications;

� in case a program does not run properly, verify the installation of the

latest .net and c/c++ redistributable libraries and executables.

After the preliminary steps, the user needs to create a workspace of

both pockets and ligands, it is important that both proteins and ligands

descriptions are in .pdb format in order to proceed: usually ligands .pdb

�les uses HETATM as structural elements: the user needs to transform

HETATM in ATOM maintaining the correct tabulation of the �le. In order

to do that, the user must use the �rst program: Protein Data Helper.

Protein Data Helper allows the user to download both proteins and ligands

from the Protein DataBank, and to prepare the .pdb �les to be used by

Protein Inspector.

First the user has to write the PDBID of the protein we want to down-

load and select the working directory as shown in �gure 1.

Then, the user selects one or (if available) more ligands. The user needs

to select a ligand ID and presses Extract Ligand Data in order to get all

the data contained inside the protein .pdb �le, then it is necessary to press

Extract Ligand Data in order to save a ligand .pdb �le compatible with

Protein Inspector. After saving all the ligands data we need to trim away

unuseful data from the original protein �le; in order to get a corrected

protein �le the user needs to select Save �ltered PDB. The results of these

operations are shown in �gure 2 and �gure 3. All these operations are

2 Chapter 1. System Tutorial and Manual

Figure 1.1 � Protein Data Helper �rst steps

Figure 1.2 � Protein Data Helper: saving .pdb �le and extracting ligand data

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mandatory in order to use Proteins Inspector. With this second software

the user can extract both a 3D representation of a pocket or a ligand, and

also their parameters data. The user needs to check some checkboxes �rst,

see �gure 4 for a possible default combination of checkboxes. After setting

the program the user select Pocket Batch, wait for program ending and

�nally select Record Pocket to obtain both .obj �les and parameter data

�les. These operations can be executed as many times as necessary in order

to de�ne and create a set of pockets and ligands. If the user as prepared all

the data �rst, he can also select Record Pocket All to do a batch analysis.

The next step is to use Object to E.G.I. Visualizer to test these �les in

order to �nd possible matches; this is a crucial step and must be prepared

carefully. At �rst the user needs to copy all the .obj �les (both pocket and

ligand ones) inside the "Obj" directory inside the program's main folder,

this operation ensures that the program can read the 3D models' geometrical

and biochemical data. Then the user has to set the con�guration �le to �t

his/her needs. Please refer to �gure 5 for a detailed explanation of all the

commands inside the con�guration.txt �le.

Figure 1.3 � Data Helper: saving corrected .pdb data for Proteins Inspector

As can be seen from the text �le the user needs to select the visual

modality of the program at �rst:


Figure 1.4 � Proteins Inspector: default con�guration

1. Auto: the program reads the test �les inside its folder and does all the

evaluations automatically. This is the preferred modality for testing

purpose and the one that this tutorial will explain in details;

2. Screen (Console): this modality uses console commands to do the

work, but requires user interaction; it is particularly useful when the

user doesn't require graphic support or in case of slower systems;

3. Gui: this is the Graphical Interface mode with which the user can

directly see the result of all his/her operations (model loading, E.G.I.

creation, result values). This modality is used mostly for presentation

and discussion purpose.

The next two lines are used for de�ning the current text �le, but in this

tutorial the user will be presented with a method that generates automat-

ically this set of information. After that there are the test options (Test

Type, Test Options, Activate Bounding, Bounding Type, Level of Subdivi-

sion), these will be also generated automatically. What the user needs to

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Figure 1.5 � ObjectToEGI Visualizer con�guration �le

do is just to set up the program mode to Batch (value: 2) and use the Pro-

teinFilesManager program. Running the Test File Creation executable

the user will be presented with the interface of �gure 6

First the user needs to de�ne the paths of the .obj �les directory de-

scribed before and the destination directory, than he must select what data

needs to be extracted. Then the user will be presented with the possibility

to choose from various options to drive the test and also (very important)

the possibility to pre-�lter the pockets based on their volume and conserva-

tion's value. Figure 6 presents a default con�guration. After all the options

have been set, the user can select RUN to generate a complete test �le with

all the pockets and ligands de�ned with Proteins Inspector. The next step

is to use Test Helper program; please refer to �gure 7 for a detailed view of

the steps for using this software.

The result �les contain a list of possible pockets candidates for pocket-

ligand docking with the speci�ed ligand; �gure 8 shows a possible result

�le.

The result �le shows a set of possible couple sorted from the most prob-

able (top) to the less probable (bottom). It is interesting to notice that the

�rst couple in this particular case is a perfect match because pocket and

ligand are from the same complex. The results can be further re�ned with

the Test Parameters Re�ner; this software uses the set of parameters

collected from the analysis done with Protein Inspector and with this set of


Figure 1.6 � Test File Creator

information we can exclude some false positives. Please view �gure 9 for a

detailed view of Test Parameters Re�ner interface and functionalities.

The �rst step is to locate the results directory of Test Helper, then

the folders for both proteins and ligands parameters; the user also needs

to de�ne directory for saving results and which parameters use to drive

the re�nement. After all these preparation steps, the user needs to de�ne

the number of iterations for the AdaBoost algorithm and then launch the

re�nement. With the re�nement process the user can see the new candidate

positions for all the possible couples that succeeded in the test in the output

directory. Possibly the newer positions are more accurate and precise than

the older ones thus enhancing the �nal result.

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Figure 1.7 � Required steps for using Test Helper

Figure 1.8 � Result �le of ObjectToEGI Visualizer

1.0.1 Optional programs tutorials

This section covers an example on how to use the Black Mambah Frame-

work.

How to use Black Mambah Framework

Black Mambah Framework is essentially a collection of shortcuts for the

other programs, what the user needs to do is simply de�ne all the paths of

the executable �les the �rst time and save the con�guration, then he/she

can use this software to load directly the other ones. Please simply refer to


Figure 1.9 � Detailed view of Test Parameters Re�ner

�gure 10 and �gure 11 for a complete overview of the system.

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Figure 1.10 � Black Mambah Framework main interface

Figure 1.11 � Con�guration window

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