Shape Complementarity (SC) (Lawrence and Colman, 1993) is a measure of "goodness of fit" between two protein interfaces. It ranges from 0 to 1, where 1 is maximum compatibility. It relies on the relative shape of the two interfaces between each other. It has been utilised to explore the relation ship between antibody/T-cell receptor and antigen.
Buried Surface Area (BSA; reviewed by Ali et al., 2014) is a geometric quantity that measures to total surface area (in Å2) of a complex buried within another complex. Available Surface Area (ASA) is the reciprocal; that is, the total surface area accesible. This calculation of accessibility is generally calcualted in relation to solvent acessible surface area (SASA). SASA imagines that a ball of a given radius is rolling along the surface ofthe protein of interest. If there is sufficient geometric space to allow the solvent to pass unimpeded it said to be accessible.
This tool calculates ASA by using the Shrake Ruplley algorithm implemented in Biopython. It then computes BSA by calculating the ASA of the complex of interest unbound to the other complexes in the structure and comparing the two numbers.
This tools is designed to be used as both a standalone tool and a module to be imported.
pip3 install .
There are two functions SCASA sc, which calculates SC and SCASA asa which calculates ASA. There are 3 common argumemnts:
--pdb INFILE, -P INFILE
PDB file of a complex
--complex_1 COMPLEX_1, -C1 COMPLEX_1
Chains of first complex, corresponding to the chains in the PDB file. If supplying
multiple chains they must be a single uninterrupted chain e.g. --complex_1 ABC
--complex_2 COMPLEX_2, -C2 COMPLEX_2
Chains of first complex, corresponding to the chains in the PDB file. If not supplied the
default would be all remaining chains
--level ASA_LEVEL, -L ASA_LEVEL
The specific flags for sc are:
--distance DISTANCE, -D DISTANCE
Distance parameter used for generating an interface between the two surfaces. Atoms with
no neighbours within this range are excluded
The specific flags for sc are:
--level ASA_LEVEL, -L ASA_LEVEL
Level to calculate ASA and BSA to. They can be 'S' for complex, 'C' for chain 'R' for
residue, or 'A' for atom
So to run sc an example command line argument would be: SCASA sc --pdb test/data/1FYT.pdb --complex_1 DE --complex_2 CAB --distance 4.0. and
an example for asa would be SCASA asa --pdb test/data/1FYT.pdb --complex_1 DE --complex_2 CAB --level R.
SCASA can be imported as a module using import scasa.