Version 1.0

Refinement  

Demo | Example PDB File

AIR provides an iterative refinement process to improve the superposition quality of aligned results obtained from your own MStA systems. The coordinate information of aligned proteins should be stored within a standard PDB file format. For example, if there were 5 structures aligned by your own algorithms, save 5 different structures' coordinates in different chains. You can use REMARK tag to annotate the corresponding relationship between original proteins and chain IDs. The structural information of residues for each protein is exactly the same as the PDB format. Partial contents of this example are shown as the follows:

REMARK A:1ONI:A
REMARK B:1QD9:A
REMARK C:1DBF:A
REMARK D:1UFY:A
REMARK E:1JD1:A
ATOM      1  N   SER A   2     -23.642  -2.099  21.755  1.00 52.81           N
ATOM      2  CA  SER A   2     -22.480  -3.026  21.611  1.00 52.41           C
ATOM      3  C   SER A   2     -22.040  -3.210  20.148  1.00 51.22           C
ATOM      4  O   SER A   2     -21.117  -3.973  19.863  1.00 51.19           O
ATOM      5  CB  SER A   2     -22.838  -4.385  22.211  1.00 52.77           C
ATOM      6  OG  SER A   2     -21.670  -5.156  22.451  1.00 55.57           O
ATOM      7  N   SER A   3     -22.764  -2.647  19.203  1.00 49.49           N
ATOM      8  CA  SER A   3     -22.344  -2.761  17.837  1.00 48.72           C
ATOM      9  C   SER A   3     -21.292  -1.724  17.406  1.00 47.04           C
ATOM     10  O   SER A   3     -21.156  -0.668  18.024  1.00 46.57           O
ATOM     11  CB  SER A   3     -23.567  -2.706  16.938  1.00 48.91           C
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Once the input file is constructed, input the PDB file to AIR and click on "Run" button. The system will execute the iterative refinement processes and display the original aligned structures in left window and refined structures in the right window. All iterative results for each round will be displayed in the bottom text box.