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:

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,

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. 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.

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