CV_shave: protein shaving

Mihaly Mezei

Department of Pharmacological Sciences,

Icahn School of Medicine at Mount Sinai

New York, NY 10029

Aug 25, 2020.

The program reads a file containing a list of PDB files to analyze. For each protein domain (chain) in the PDB file the program removes one by one the outermost heavy atom. The atom with the larges circular variance (CV) is considered to be the outermost.

Whenever the atom removed is part of the backbone, and the nearest (or end) break residue is more then a user-specified number of residues (break residue distance) away the residue it is part of is marked as a special one - tentatively suggested to be an Achilles' heel. The program lists all of these residues during the run.

At the end of the run phe program prints (broken down by secondary structure element and overall)

Also correlations between the two kind of preak point propensities and side chain length, amino acid volume and hydrophobicity are also calculated.

The program can be run as
cvshave [directive argument] [directive argument]...
-lfFile listing the PDB files to process 
-cvCV cutoff15.0
-rdBreak residue distance10
-ivOutput level1
-nsNumber of files to skip0
-nsNumber of files to processall
-ofOutput filecvshave.out

If only the program name is typed, the user will be promptes for the input information.

The program is written in Fortran-77 and can be compiled with any Fortran compiler, including GNU fortran:

f77 -o cvshave cvshave.f

to obtain the executable cvshave