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Virtual screening method PharosDre@ms3 is the compound virtual screening tool
Simulations can be used to derive new drug candidates for protein targets.

PharosDre@ms3 Client Installation

1. Download the installation file
You can download it by clicking on the PharosDre @ ms3 download button on the bottom left of the main screen or by clicking 'here'.
2. Installation
Run the downloaded installation file to install it.

PharosDre@ms3 설치화면

Running and connecting to the PharosDre@ms3 client

A license file is required to run the PharosDre @ ms3 client, and licenses are issued only to paid members.
1. Licensing
Change the name of the issued license to 'License.lic' and copy the file to the '../License' folder under the installation folder (../License/License.lic).
2. Login
When you run PharosDre@ms3, a login window appears.
Enter your Chemiverse website ID and password here.
3. Main Screen
If you connect normally, you can check the PharosDr@ms3 main screen.
Depending on the network conditions, it may take some time to connect.

Screen Layout

PharosDre@ms3 화면구성

1. Icon menu
You can conveniently use the most popular features of PharosDr@ms3.
2. Hierarchy
You can see a structured list of the items you have imported (protein structure, compound structure, etc.) and the items you have created (binding site, pharmacophore, etc.).
3. Structure Viewer (Viewer)
All visual information including protein / compound structure can be checked.
4. Sequence Viewer
Homology modeling, Point mutation, Protein sequence information required for study.

Tutorial 1 - Protein Structure-Based Virtual Discovery

단백질 구조 불러오기

1. Execute 'File> Open PDB from URL' to import the protein structure.
- Open 'File> Open PDB from URL' in the top menu and enter 1V4S.
- Open PDB from URL: Retrieves the protein structure from the RCSB PDB database.
- Open: Loads the protein structure stored in the user's PC.
2. Enter 1V4S in the Open PDB from URL window.

Binding site 탐색

3. Under Hierarchy, select 1V4S.
4. Run a protein structure-based binding site search.
The same is true for 'Tools> Binding Site by Receptor-based' in the top menu.

Pharmacophore생성

5. Select 1V4S_Site_01 binding site.
6. Create a Receptor Pharmacophore.
The same is true when you run 'Tools> Tools> Pharmacophore> Receptor Pharmacophore' from the top menu.

가상탐색 실행

7. Select the desired feature of the discovered Pharmacophore.
* You can select multiple items using Ctrl key. *
* If the number of features is less than 4, the virtual search time may take a very long time. *
8. Select and run the Virtual Screening icon.
The same goes if you run 'Tools> Tools> Virtual Screening' from the top menu.
9. Enter the Virtual Screening setting value and press the OK button to execute the virtual search.
In Docking Type, Rigid Ligand is an option that does not perform minimization and Flexible Ligand is an option to perform minimization.
Project Name and Job Name are required.
Database allows you to select both the compound database provided by the Chemiverse web service and the user-generated subset.


가상탐색 결과확인

10. Check the virtual search results on the Chemiverse web page (* attached image is not relevant to actual results).
You can check it in 'Service> Compound search> Virtual search'.
A: Select the name to identify the resulting compound
B: "Download" the work environment file (PharosDre @ ms3 session file, * .pds)
C: "Download" the resulting compound structure file (* .sdf)

Tutorial 2 - Ligand (Compound) Structure-Based Virtual Discovery

PDB 사이트에서 리간드 sdf 다운로드

1. Prepare a ligand (compound) sdf file (sample download).
Go to www.rcsb.org, search for 1V4S, and download the sdf file.

단백질 및 화합물 불러오기

2. Call up the protein structure and ligand structure from the PharosDre@ms3 client.
- Import protein structure: After executing 'File> Open', select * .pdb in the bottom right or 'File> Open PDB from URL' and input PDB ID
- Loading compound structure: After selecting 'File> Open', select * .sdf from the bottom right.

단백질 및 화합물 불러오기

3. In the Hierarchy, select 1V4S (Protein) and 1V4S_MRK_00001 (Chemical).
4. Run a binding site search based on the ligand structure.
The same goes for 'Tools> Binding Site by Ligand-based' in the top menu.

Pharmacophore 생성

5. Select the Binding Site to identify the binding site generated around the compound structure.
6. In Hierarchy, select 1V4S_MRK_00001 and 1V4S_site_ligand together.
7. Run the Ligand Pharmacophore.
The same goes for 'Tools> Pharmacophore> Ligand Pharmacophore' in the top menu.

가상탐색 실행

8. Select the desired feature of the discovered Pharmacophore.
* You can select multiple items using Ctrl key. *
* If the number of features is less than 4, the virtual search time may take a very long time. *
9. Select and run the Virtual Screening icon.
The same goes if you run 'Tools> Tools> Virtual Screening' from the top menu.
10.. Enter the Virtual Screening setting value and press the OK button to execute the virtual search.
In Docking Type, Rigid Ligand is an option that does not perform minimization and Flexible Ligand is an option to perform minimization.
Project Name and Job Name are required.
Database allows you to select both the compound database provided by the Chemiverse web service and the user-generated subset.


가상탐색 결과확인

11. Check the virtual screening results on the Chemiverse web page (* attached image is not relevant to actual results).
You can check it in 'Service> Compound search> Virtual search'.
A: Select the name to identify the resulting compound
B: "Download" the work environment file (PharosDre @ ms3 session file, * .pds)
C: "Download" the resulting compound structure file (* .sdf)