Computational Chemical and Structural Biology
BCL::CreateSSEPool is a C++ based application, created by Vanderbilt University's Meiler Laboratory, which ispart of a larger library of applications called BCL::Commons. BCL::CreateSSEPool generates the secondarystructure pool for given proteins using individual and consensus secondary structure predictions. The application first reads a fasta file as input, then reads secondary structure predication parameters entered in the commandline, and finally creates the secondary structure pool. The output is an ASCII files that shows the predicted SSEs based on input paramaters.
VI. RUNNING BCL::CreateSSEPool.
Running BCL::CreateSSEPool consists of three main steps.
1) Create the fasta sequence file for the protein to be studied:
You will need the protein sequence in fasta format, and it should be stored in a <.fasta> file. An example is given below. For more information about fasta formats, please visit http://www.ncbi.nlm.nih.gov/Blast/fasta.shtml.
2) Create the Secondary Structure Prediction Files or use PDB format for protein to be studied:
3) Run BCL::CreateSSEPool:
At a command prompt, navigate to the location of your BCL::CreateSSEPool executable program. The syntax for running the application looks like the following:
bcl.exe CreateSSEPool -prefix -ssmethods -factory
BCL::CreateSSEPool needs a fasta sequence with the extension <.fasta> and a secondary structure element (sse)file type to exist in the same directory.
The allowed file types and parameters -help flag.
INPUT AND OUTPUT.
BCL::CreateSSEPool requires two inputs, a fasta file and a corresponding sse prediction type. The fasta file uses one letter codes for protein sequence and looks like the following:
The allowed sse prection type files are listed in the -help flag.
The output file is formatted as following:
HELIX 1 1 GLY A 98 ALA A 108 1 11
HELIX 2 2 GLY A 98 LYS A 120 1 23
SHEET 3 GLY A 100 SER A 106
HELIX 4 4 ASP A 110 LYS A 120 1 11
HELIX 5 5 ASP A 113 ARG A 123 1 11
HELIX 6 6 SER A 127 ASN A 138 1 12
HELIX 7 7 SER A 127 LEU A 150 1 24
SHEET 8 SER A 128 ASN A 131
HELIX 9 9 SER A 133 ILE A 142 1 10
The individual columns represent following:
Column 1: Secondary structure type
Column 2: Secondary structure number
Column 3: Helix number
Column 4: Three letter amino acid code at first position of SSE
Column 5: Chain type
Column 6: Starting Amino Acid position of SSE
Column 7: Three letter amino acid code at last position of SSE
Column 8: Chain type
Column 9: Ending amino acid position of SSE
Column 10: Helix type
Column 11: Length of SSE
Helpful information concerning syntax and flags can be obtained by typing bcl.exe CreateSSEPool -help
For more general information about the product, type bcl.exe CreateSSEPool -readme
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