AIDA Server Help Page

1. How can this server help you?

• If you have domain structures and don't know how they should be arranged.

• If you only have the sequence and don't have any information on domain numbers and boundaries.

2. Regarding the input fasta sequence:

• Submit one sequence at a time.

• AIDA itself has no limit regarding the maximum sequence length. It does, however, rely on PSIPRED's secondary structure prediction result which is limited to sequence of 10,000 residues or less.

• You can provide sequences with or without the fasta ">" header line.

3. Regarding the domain structures:

• Domain structures should be compressed as one file. The name of the ith domain is pmodeli.pdb.

• While the AIDA executable program has no limit on the maximum number of domains the online AIDA server sets it to 20.

• Residue numbers in each domain models correspond to their positions in the input fasta sequence. Numbering starts at 1.

• Two residues at each end of the domain model are treated as the linker region by default, which are completely flexible during the simulation. User can remove coordinates of more residues in the two ends of each domain structure.

4. Regarding the assembly of discontinuous domain:

• There should be exactly three input domain structures in the compressed file uploaded by the user.

• The first and third domains form the discontinuous domain while the second is the inserted domain. Relative position/orientation of the first and third domains will stay fixed during the AIDA simulation.

5. Regarding the distance restraints:

• Distance is given between Cα atoms.

• The first and second values are residue numbers while the third value is their distance in Angstroms.

6. Regarding the output page:

• The output page will contain the assembled structure if the user provides domain structures. Different domains are in different colors. The linker region is in red.

Click [example1] to see an example of assembly of 4 continuous domains.

Click [example2] to see an example of assembly of 1 continuous domain with 1 discontinuous domain.

• Additionally, AIDA will output secondary structure prediction result and alignments with the top PDB templates selected by FFAS-3D if the user only provides the sequence.

Click [example3] to see the automated prediction of a single-domain protein.

Click [example4] to see the automated prediction of a protein with 2 continuous domains.

Click [example5] to see the automated prediction of a protein with 1 continuous domain and 1 discontinuous domain.