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What is this website for?

ToSY is an integrated computer program to predict a 3D structure of two proteins/domains in complex form. The input data should be one of the followings;

  • The 3D structures of two proteins/domains,
  • the 3D structure of one protein/domain and the amino acid sequence of one protein/domain,
  • the amino acid sequences of two proteins/domains.
The provided amino acid sequence undergoes a comparative modeling procedure. When a 3D structure of the amino acid sequence can be modeled, then the docked structure is predicted.

It is user's responsibility to make sure that the proteins/domains do interact. This server assumes that the proteins/domains interact with each other and provides candidate docked 3D structures.

A simple tutorial for this website is found here (tutorial in Japanese is here).

Input data and Run
1. Upload either (2 PDB files), (1 PDB file and 1 FASTA file) or (2 FASTA files),

 3D Structure   ( PDB format )
Upload PDB 1:    Download sample data 1

Upload PDB 2:    Download sample data 2

amino acid sequence   ( FASTA format )

Upload 1 or 2 sequences in a single file

or paste 1 or 2 sequences
2. Fix the options,

Specify the type of input data.
If two data are domain structures, select domain, if protein structures, select protein, and if a mixture, select protein.
           protein     domain
Specify the number of decoys.
The more, the more precise, but it takes time to predict:      
Specify the number of alternative outputs.
The number of structures from the top score:      
3. Register the data receiver,

The result will be notified by E-mail.    (Sample result)

E-mail:
Password to get the result.                              
Do not cut-and-paste. Retype the password.      Keep the password, or the result cannot be retrieved!
4. And run.
             
Links to related websites

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