Molecular Modeling and Bioinformatics

SHEBA (Structural Homology by Environment-Based Alignment)

Examples

I. Convert (.pdb) to (.env) Format:

%sheba -e 1EVH.pdb

Output:

The (*.env) file is created in the same directory and the content is like this:

If the PDB file is from NMR experiment, there might be more than one model of the structure in that pdb file. SHEBA only takes the first model and converts it into (*.env) format. Here is an example:

II. Pair-Wise Comparison of Two Structures:

SHEBA has several options for one-to-one comparison in terms of output. Input files can be *.pdb or *.env format. Here we take two protein domains, 1EVH (contractile protein EVH1 domain) and 1DDW (homer of EVH1 signaling protein), as an example.

1. Default Output:  Back to Manual

%sheba 1EVH.pdb 1DDW.pdb

Output:

2. Formatted Row Output:  Back to Manual

%sheba -r 1EVH.pdb 1DDW.pdb

Output: 

3. Formatted Column Output:  Back to Manual

%sheba -c 1EVH.pdb 1DDW.pdb

Output:

4. Simple Column Output:  Back to Manual

%sheba -g 1EVH.pdb 1DDW.pdb

Output:

5. Create Transformation Matrix:  Back to Manual

%sheba -x 1EVH.pdb 1DDW.pdb

Output:

The transformation matrix is stored in another file (.trf) in the same directory and can be used for transformation process with -t option. The content in the (.trf) is

The transformed coordinates can be represented as

X' = T1 + M * ( X - T2)

X is the position before transformation and X' is the position after transformation.

T1 is the first row of the transformation matrix and T2 is the last row. M is the 3x3 matrix in the middle.

6. Transform the Structure According to the Transformation Matrix:  Back to Manual

%sheba -t 1EVH.pdb 1DDW.trf

Output:

The transformed (.pdb) or (.env) file is stored in the same directory with "pdb" extension. Only the coordinates of each residue are different from the original file. The content is like this:

7. Permuted Alignment:  Back to Manual

%sheba -p 1EVH.pdb 1DDW.pdb

Output:

8. Change the Number of Iteration:  Back to Manual

Put the number of iterations after -i operation. Increasing the number of iterations may get better superposition but takes longer time if the number of structures to be compared is large; also, we found it does not vary much after iterating 3 times so the default is set to 3.

%sheba -i 5 1EVH.pdb 1DDW.pdb

Output:

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