Help for using FTALIGN server

1. Structure input

The FTALIGN server is to align two protein structures by using a fast Fourier transformation (FFT)-based topology-independent and global structure alignment algorithm. The input structure can contain one protein chain or multiple chains. Due to its truly global search nature, FTALIGN is guaranteed to find the globally optimal alignment between two molecules. Users are required to provide the three-dimensional (3D) structures of two molecules to be aligned. The FTALIGN server accepts two types of input for the molecules:

• Upload your pdb file in PDB format.
• Provide your pdb file in PDB ID:ChainID (e.g. 256B:A).

Only ONE type of input is needed for each molecule.

If more than one type of input are provided, the first one will be used. If the uploaded pdb file contains multiple models like the following,

MODEL  1
...
ENDMDL
MODEL  2
...
ENDMDL
...

only the first model will be used for alignment. For the "PDB ID:ChainID" input, users can provide one single chain ID or multiple chain IDs. For example, "256B:A" stands for the chain A of the pdb file of 256B; "256B:AB" stands for the chains A and B of the pdb file of 256B.

Number of alignments: By default, the server only outputs the top alignment with the highest match score. However, it also offers users an option to obtain up to 10 alternative alignments with a high match score, which is sometimes useful for conformational change and/or funtional analysis of proteins.

2. About the results

After an alignment job is completed, FTALIGN will provide three types of files for download.

• Two input pdb files named "molA.pdb" and "molB.pdb".
• The aligned pdb file(s) of the second protein, named like "ALign1.pdb", "Align2.pdb", .... Users can view an alignment by opening the first protein "molA.pdb" and an aligned pdb file like "Align1.pdb".
• The residue alignment file(s) of two molecules, named like "ALign1.txt", "Align2.txt", ..., which read like the following

	  55    78      55  SER  78  PHE
	  56    79      56  PRO  79  GLN
	  57    80      57  GLU  80  ASN
	  58    81      58  MET  81  MET
	  59    82      59  LYS  82  GLU
	  60    83      60  ASP  83  ASP
	  61    84      61  PHE  84  VAL
	  62    85      62  ARG  85  GLY
	  63    86      63  HIS  86  LYS
	  64    87      64  GLY  87  ILE
	  65    88      65  PHE  88  ALA
          ......

where each line stands for a one-to-one residue equivalence, and the file is self-explanatory.

All the above results can be downloaded as a compressed package.

Alignment Visualization: In addition, the server also provides users a web interface to interactively view the structure alignment(s) betwee two molecules.