Tutorial in bSiteFinder

In this tutorial we will introduce bSiteFinder applications. The tutorial has been broken down into the following steps:

Performing a binding site prediction

• Enter email address

• Select and upload your query file(s)

• Submit the task

• Result(s)

Browsing and downloading your result(s)

• Bound chain prediction result

• Unbound chain prediction result using Homology Indexing

• Unbound chain prediction result using Chain Length Indexing

• Downloading your result(s)

Performing a binding site prediction

1. Enter email address:

First enter an email address for result feedback. If the email address is valid, there will be a check mark.

2. Select and upload your query file(s):

Click the "SELECT PDBs..." button, and upload your own pdb files.

3. Submit the task:

Click the "Submit" button, and finish the submission of the task.

4. Result(s):

If the calculation is done, result will be displayed in "Done List" and a notification email with result URL will be sent to you.

Result(s) in "Done List".

Notification email with result URL.

Browsing and downloading your result(s)

1. Bound chain prediction result (5p2p as example):

Conventions used in bound chain prediction result files:

Download in detail page File name File content
Binding Site Info File that end with "json" information of binding site
Query Chain File that begin with "QRY_" pdb format file of chain in query
 

Browsing your result(s):

Result in detail page. If multiple chains are given in one query, the chain displayed can be chosen at "Chain List". Result of each chain can be contained respectively.

Result of each chain in the query will be contained in a folder.

Result of each binding site in the chain will be contained in a folder.

Result of each bound chain will create two files.

2. Unbound chain prediction result using Homology Indexing (3p2p as example):

Conventions used in unbound chain prediction result files:

Download in detail page File name File content
Binding Site Info File that end with "json" information of binding site
Query Chain File that begin with "QRY_" pdb format file of chain in query
Aligned Template Chain File that begin with "ALN_TPL_" pdb format file of aligned template chain with ligand
Query and Aligned Template Chain File that begin with "QRY_ALN_TPL_LIG_" pdb format file of both chain in query and aligned template chain with ligand
Query with Aligned Ligand File that begin with "QRY_ALN_LIG_" pdb format file of chain in query with aligned ligand
 

Browsing your result(s):

Result in detail page. If multiple chains are given in one query, the chain displayed can be chosen at "Chain List". Result of each chain can be contained respectively.

Result of each chain in the query will be contained in a folder.

Result of each binding site in the chain will be contained in a folder.

Result of each unbound chain will create five files.

3. Unbound chain prediction result using Chain Length Indexing (4los as example):

Conventions used in unbound chain prediction result files:

Download in detail page File name File content
Binding Site Info File that end with "json" information of binding site
Query Chain File that begin with "QRY_" pdb format file of chain in query
Aligned Template Chain File that begin with "ALN_TPL_" pdb format file of aligned template chain with ligand
Query and Aligned Template Chain File that begin with "QRY_ALN_TPL_LIG_" pdb format file of both chain in query and aligned template chain with ligand
Query with Aligned Ligand File that begin with "QRY_ALN_LIG_" pdb format file of chain in query with aligned ligand
 

Browsing your result(s):

Result in detail page. If multiple chains are given in one query, the chain displayed can be chosen at "Chain List". Result of each chain can be contained respectively.

Result of each chain in the query will be contained in a folder.

Result of each binding site in the chain will be contained in a folder.

Result of each unbound chain will create five files.

4. Downloading your result(s):

Result(s) can be downloaded through "Done List" and/or notification email.

Done List:

Click pdb id to see the details of the result for each pdb file. Click "Link" button to download the whole result files.

Notification email:

Click the "Result URL" in notification email to download the whole result files.