Skip to end of metadata
Go to start of metadata

SHEBA (Structural Homology by Environment-Based Alignment)

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

%sheba -e 1EVH.pdb

Output:

convert .pdb to .env format output example

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

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: PDB file from NMR experiment 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: comparison of two structures output example

2. Formatted Row Output:  Back to Manual

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

Output:  formatted row output example

3. Formatted Column Output:  Back to Manual

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

Output: formatted column output example

4. Simple Column Output:  Back to Manual

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

Output: simple column output example

5. Create Transformation Matrix:  Back to Manual

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

Output: transformation matrix example

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

transformation matrix content example

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: transformation matrix output example

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: permutated alignment output example

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: change the number of iteration output example

NEXT PAGE: Multiple Alignment

Last updated by Fox, Susan (NIH/NCI) [E] on Jun 21, 2011