fibos (version 2.0.1)

occluded_surface: Occluded Surface (OS)

Description

The 'Occluded Surface (OS)' algorithm is a widely used approach for analyzing atomic packing in biomolecules. Here, we introduce 'FIBOS', an 'R' and 'Python' package that extends the 'OS' methodology with enhancements. The homonymous function 'occluded_surface' calculates 'OS' per atom.

Usage

occluded_surface(pdb, method = "FIBOS", density_dots = 5)

Value

A table containing:

ATOM

the atomic contacts for each atom.

NUMBER OF POINTS

the number of dots (patches of area) on atomic surface.

AREA

the summed areas of dots.

RAYLENGTH

the average lengths of normals normalized by 2.8 \(\text{\AA}\) (water diameter). So, raylen is a value between 0 and 1. A raylen close to 1 indicates worse packaging.

DISTANCE

the average distances of contacts in (\(\text{\AA}\)).

Arguments

pdb

4-digit PDB id (will fetch it from the RCSB repository) or the path to a PDB local file.

method

Method to be used: 'OS' (classic) or 'FIBOS'(default).The classic 'OS' covers the surface radially with one of the axes as a reference when allocating the dots. In 'FIBOS', Fibonacci spirals were used to allocate the dots, which is known to produce lower axial anisotropy as well as more evenly spaced points on a sphere.

density_dots

Distribution density of atomic dots for surface occlusion calculation.

Author

Herson Soares, Joao Romanelli, Patrick Fleming, Carlos Silveira.

Details

'Occluded Surface (OS)' (Pattabiraman et al. 1995) method distributes dots (representing patches of area) across the atom surfaces. Each dot has a normal that extends until it reaches either a van der Waals surface of a neighboring atom (the dot is considered occluded) or covers a distance greater than the diameter of a water molecule (the dot is considered non-occluded and disregarded). Thus, with the summed areas of dots and the lengths of normals, it is possible to compose robust metrics capable of inferring the average packing density of atoms, residues, proteins, as well as any other group of biomolecules.

For more details, see (Fleming et al, 2000) and (Soares, et al, 2024)

References

Fleming PJ, Richards FM (2000). "Protein packing: Dependence on protein size, secondary structure and amino acid composition." doi:10.1006/jmbi.2000.3750

Pattabiraman N, Ward KB, Fleming PJ (1995). "Occluded molecular surface: Analysis of protein packing." doi:10.1002/jmr.300080603

Soares HHM, Romanelli JPR, Fleming PJ, da Silveira CH (2024). "bioRxiv, 2024.11.01.621530." doi:10.1101/2024.11.01.621530

See Also

osp()

Examples

# \donttest{
library(fibos)

#Configure the environment
fibos_config()

# Calculate FIBOS per atom and create .srf files in fibos_files folder
pdb_fibos <- occluded_surface("1ptx", method = "FIBOS", density_dots = 5.0)

# Calculate OSP metric per residue from .srf file in fibos_files folder
pdb_osp <- osp(fs::path("fibos_files","prot_1ptx.srf"))
# }