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3D-Match

3D-Match implements pairwise protein structure alignment.

The algorithm implements a three-step procedure for aligning protein three-dimensional structures. The procedure includes building of the alignment core with the optimal RMSD, its expansion by introducing new protein fragments into the alignment, and optimization using dynamic programming to finally achieve an optimal alignment. 3D-Match aligns two polypeptide chains using C-alpha atomic coordinates, secondary structure characteristics are additionally used to weight the alignment.

The input is the PDB file and the polypeptide chain identifier for each protein of a queried pair. In the case when the chain identifier is not provided, a protein structure comparison is performed using the first polypeptide chain found in the protein.

The user may visualize the structural alignment in online mode using 3D-Explorer, a program for the visualization of macromolecular spatial structures.

To visualize the structural alignment, uncheck the "Run without visualization" box.

Output data.
Structural alignment is represented in PDB format in which the queried structures are assigned different chain IDs. The values for the RMSD, Zscore and structure-based sequence alignment are accommodated in the REMARK field.

Zscore is a measure of the statistical significance of the structural alignment of the queried proteins relative to an alignment of random structures. As a rule, the score for proteins with a similar fold will be 3.5, even better than that.

An example of output data.
HEADER    PROTEIN STRUCTURE ALIGNMENT	
COMPND    (A) 1BWW chain A (B) 2BFV chain L
REMARK   1
REMARK   1 RMSD on Ca-atoms:  0.791 angstrom
REMARK   1 Zscore          :  6.230 
REMARK   1      
REMARK   1      
REMARK   1 Alignment
REMARK   1      
REMARK   1 3     DIQMTQSPSSLSASVGDRVTITCQASQDII-----KYLNWYQQKPGKAPKLLIYEASNLQ
REMARK   1 1     DIELTQSPPSLPVSLGDQVSISCRSSQSLVSNNRRNYLHWYLQKPGQSPKLVIYKVSNRF
REMARK   1      
REMARK   1 58    AGVPSRFSGSGSGTDYTFTISSLQPEDIATYYCQQYQSLPYTFGQGTKL
REMARK   1 61    SGVPDRFSGSGSGTDFTLKISRVAAEDLGLYFCSQSSHVPLTFGSGTKL
REMARK   1      
ATOM      1  N   THR A   1     -18.648   5.701 -17.803  1.00 67.85           N
ATOM      2  CA  THR A   1     -18.151   6.056 -16.472  1.00 64.75           C
ATOM      3  C   THR A   1     -16.630   6.135 -16.463  1.00 48.48           C
ATOM      4  O   THR A   1     -15.942   5.184 -16.867  1.00 47.02           O
ATOM      5  CB  THR A   1     -18.621   5.088 -15.373  1.00 72.33           C
ATOM      6  OG1 THR A   1     -19.566   4.118 -15.842  1.00 76.14           O
ATOM      7  CG2 THR A   1     -19.338   5.863 -14.272  1.00 80.20           C
ATOM      8  N   PRO A   2     -16.032   7.229 -16.013  1.00 34.29           N
ATOM      9  CA  PRO A   2     -14.555   7.266 -16.013  1.00 29.06           C
ATOM     10  C   PRO A   2     -14.037   6.265 -14.977  1.00 29.14           C
ATOM     11  O   PRO A   2     -14.654   6.023 -13.941  1.00 27.39           O
ATOM     12  CB  PRO A   2     -14.217   8.680 -15.566  1.00 28.31           C
ATOM     13  CG  PRO A   2     -15.493   9.424 -15.458  1.00 30.57           C
ATOM     14  CD  PRO A   2     -16.595   8.410 -15.368  1.00 32.32           C
ATOM     15  N   ASP A   3     -12.875   5.683 -15.224  1.00 27.28           N
ATOM     16  CA  ASP A   3     -12.313   4.811 -14.192  1.00 21.41           C

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