AmbitXT v2.2.0 User Manual, Vodiči, Projekti, Istraživanja od Biohemija

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AmbitXT v2.1.

Manual

June 2009

Table of Contents

• Introduction
  • Functions of AMBIT XT v2.1.0
  • Workflow of AMBIT XT v2.1.0
• Using Database Utilities
  • General Information
  • Prerequisite for using Database Utilities
  • Getting connected
  • Importing structures
  • Importing properties
  • Calculating fingerprints and descriptors
• Using REACH PBT & vPvB Assessment
• Using Profile & Category
  • General Information
  • Prerequisite for using Profile & Category
  • Building a category............................................................................................................................
  • Exporting results
• Using Simple Search
  • General Information
  • Prerequisite of Simple Search
  • Using search
  • Using Advanced search
  • Refine search results
  • Browse previous search results
  • Displaying Properties
  • Exporting search results

• Admin

Each module performs individually without influencing other modules.

Workflow of AMBIT XT v2.1.

AMBIT XT v2.1.0 communicates with the users via the workflow window. Each workflow step will be indicated by one of the following symbols:

= This step has been successfully done and the answer of the question/condition is YES.

= This step has been successfully done and the answer of the question/condition is NO.

= Pending till all the conditions are fulfilled.

= This step is successfully done.

When an error occurs, it is recommended to always check with the last workflow step performed and restart accordingly.

Using Database Utilities

General Information

Database Utilities controls and manages the AMBIT databases. Its main functions include:

• Importing structure / properties

into the database;

Calculating fingerprints and descriptors for structures

in the database;

Control MySQL server;

Generates database statistics

, and

Prerequisite for using Database Utilities

Manage templates and properties.

• Stable Internet connection

Getting connected

You must log into the database in order to perform all the functions in this module.

Double click Database tools > MySQL start

AMBIT XT v2.1.0 comes with a default user ‘guest’ with password ‘guest’ in the default database ‘ambit2’. You can check your connection status in the status window:

3. Click to select your matching criteria (e.g. to match by CAS registry number; EINECS registry number, PubChem Compound ID, InChi or SMILES), then click Next;
4. Configure the dataset i.e. name, reference etc. in the prompted window, then click Next.

The importing process might take few minutes or longer depending on the size of imported file, pay attention to the process indicator bar at the right corner:

The completion of importing process is indicated in the Database tools window as below:

DO NOT log out while it is still moving!

Using REACH PBT & vPvB Assessment

Please download the independent user manual for REACH PBT & vPvB Assessment from AMBIT XT v2.1.0 website.

Using Profile & Category

General Information

Profile & Category allows the users to build the category with individual profile e.g. properties, endpoints or descriptors and comparing the similarities among selected substances under different criteria. This module is still under development in AMBIT XT v2.1.0.

Prerequisite for using Profile & Category

• AMBIT database is connected

Building a category

1. Double click Workflows > Category building ;
2. Click to define the structure(s) in the prompted window;
3. Follow the instructions in the prompted windows accordingly;
4. To complete structure definition, click to select No, the set of target structure is complete , then Next;
5. To complete profile definition, click to select Quit profile definition, it is complete , then Next.

The results will be shown in the Profile & Category main window as two pages: Target chemical(s) and Source chemical(s).

You can sort out the result in different ways, such as ascending by metric. Press the buttons accordingly and click to select from the drop-down selections:

Exporting results

To save the result as a file:

1. Double click Workflows > Export results ;
2. Click <…> to choose file location, type file name and select the file type as PDF/RTF/HTML/SDF in the prompted window, then click Next.

Using Simple Search

General Information

Simple Search provides a comprehensive yet efficient searching function throughout the AMBIT database. Various search criteria can be defined and different display options for search results can be selected and exported e.g. as PDF file.

Prerequisite of Simple Search

• AMBIT database is connected

Using search

Simple search is suitable when a fast and general search in the database is needed.

To use simple search:

1. Double click Workflows > Search ;
2. Select Field name and Condition from the drop-down selections and type the value (i.e. substance name) accordingly in the prompted window, then click Next ;
3. Click to select the search scope in the prompted window (Entire database; Last results; Previous search results or Datasets), then Next.

The completion of searching process is indicated in the Simple Search window as below:

The search results will be shown in the simple search main window, for example:

Using Advanced search

Advanced search provides more specific digging in the database that requires definitions on various searching criteria and longer time.

To use advanced search:

1. Double click Workflows > Advanced Search ;
2. Click to select the type of query in the prompted window, then click Next ;
3. Select Field name and Condition from the drop-down selections and type the value accordingly in the prompted window, then click Next.

The completion of searching process is indicated in the Simple Search window as below:

Refine search results

This workflow allows a refined search within the last search results.

To start, double click Workflows > Refine search results; then follow the same procedure as in the advanced search to define the search criteria.

Browse previous search results

You can have a look at the previous search results by double click Workflows > Browse previous search results.

Click to select from the previous search results list:

Exporting search results

1. Double click Workflows > Export results ;
2. Click <…> to choose file location, type file name and select the file type as PDF/RTF/HTML/SDF in the prompted window, then click Next.

The completion of searching process is indicated in the Simple Search window as below: