The FancyFlexScore

Here, you will find a short review about FancyFlexScore. Further information can be found in report pdf.
The main purpose of this project is to provide an assessment of the flexibility of a protein given its sequence. In detail, the function outputs a text file containing the flexibility scores per amino acid in addition to a graphical representation of these scores along the sequence. Furthermore, both outputs include complementary information regarding the hydrophobicity and secondary structures of the protein, to provide a comparison with parameters theoretically related to flexibility.

Prerequisites

Python Packages:

• biopython >= v.1.79
• matplotlib >= v.3.3.4
• statistics >=
• requests >= v.2.25.1
• pandas >=
• seaborn >= v.0.11.2

The above packages can be easily installed by executing the requirements.txt file:

pip install -r requirements.txt

External Programs. The following programs must be on the $PATH:

• NCBI programs (Blastp, Psiblast and makeblastdb) >= v.2.10.1+: Pairwise alignment and database creation.
• T-Coffee >= v.13.45.0: Multiple sequence alignment
• DSSP >= v.2.3.0 (mkdssp): Secondary Structure assignment.

The installation of the above programs can be automatically handle by executing the requirements.py file (linux users):

 python3 requirements.py

Running the program

The user can obtain information about the program and the arguments that should write by:

python3 fancyflexprot -h

For running the program, the user should execute:

python3 fancyflexprot -i input_file -o output_file_name -ws window_size -v

The arguments are:

• -i INFILE: Input FASTA file with one unique record containing the identifier and sequence of the protein of interest. The identifier must be a uniprot ID. Chain must be specified by: >uniprotID:chain. This argument is required.
• -o OUTFILE: Output filename without extensions. It generates two files: filename_results.csv and filename_visualization.pdf (default: results). Two more files are also generated: a PDB for homologs (located at structures/directory) and a MSA aln of target protein and PDB homologs ((located at structures/directory)). THis argument is optional.
• -v verbose: To have a follow up of the program (default: False). This argument is optional.
• -ws window_size: To change the window size when computing the flexibility score. The range of accepted values: {1,3,5,7,9,11,13}. This argument is optional (default: 7).