vanddraabe (version 1.1.1)

FreeSASA.diff: Atomic SASA difference of hydrated PDB via FreeSASA

Description

Calculates the atomic solvent accessible surface area (SASA) of the provided PDB (protein structure) using the FreeSASA application (website).

Usage

FreeSASA.diff(atoms.oi, probeRadius = 1.4)

Arguments

atoms.oi

PDB structure read into R by bio3d::read.pdb(); the base::data.frame() of pdb$atom

probeRadius

Numerical values indicating the probe radius in Angstroms for the FreeSASA application; default: 1.4

Value

A PDB list with FreeSASA (ProtOr) atomic radii placed in the occupancy (o) column and SASA values calculated using the Lee & Richards method in the b-value (b) column.

Details

The purpose of this function is to calculate and return the calculated atomic SASA for the provided PDB (protein structure) and the SASA of the protein when including the hydrating waters.

Several of the FreeSASA options are set and NOT user changeable. Specifically, no log information is returned; the -L ; the number of slices per atom is set to the FreeSASA default of 20 (Lee & Richards algorithm); each FreeSASA calculation uses four (4) threads; and the ProtOr atomic radii are used.

It might be too late if you are reading this, but it is strongly encouraged to run FreeSASAcheck() to check if the FreeSASA application is correctly installed.

References

ProtOr (Protein-Organic) atomic radii: Jerry Tsai, Robin Taylor, Cyrus Chothia, and Mark Gerstein. The packing density in proteins: standard radii and volumes. J Mol Biol, 1999, 290 (1), pp 253-266. DOI: 10.1006/jmbi.1999.2829 PMID: 10388571

SASA calculation method: B Lee, FM Richards. The interpretation of protein structures: estimation of static accessibility. J Mol Biol, 1971, 55 (3), pp 379-400. DOI: 10.1016/0022-2836(71)90324-X

FreeSASA application: Simon Mitternacht. FreeSASA: An open source C library for solvent accessible surface area calculations [version 1; referees: 2 approved]. F1000Research, 2016, 5:189 DOI: 10.12688/f1000research.7931.1 PMCID: PMC4776673 FreeSASA

Examples

# NOT RUN {
  SASA.diff <- FreeSASA.diff(atoms.oi = thrombin.1hai$atom,
                             probeRadius = 1.4)
  head(SASA.diff)
  #   uniq.atom.ids SASA.prot SASA.hetatm SASA.lost
  # 1   THR_1_L_N_1      0.00        0.00         0
  # 2  THR_1_L_CA_2      0.00        0.00         0
  # 3   THR_1_L_C_3      0.00        0.00         0
  # 4   THR_1_L_O_4      0.00        0.00         0
  # 5  THR_1_L_CB_5      1.92        1.92         0
  # 6 THR_1_L_OG1_6     11.25       11.25         0
  #
  stem(SASA.diff$SASA.lost)
  #
  # The decimal point is at the |
  #
  #  0 | 00000000000000000000000000000000000000000000000000000000000000000000+1721
  #  2 | 00000000000001111111111122222222223333333333444444445555555555566666+88
  #  4 | 00001111111122222333333333334444444455555566677777777788899999000000+23
  #  6 | 00000111111222222222223333444455556666677778889900001112222333334455
  #  8 | 001122222333344566777888999001111222223444556667899
  # 10 | 000000001233445567888990001333344567899999
  # 12 | 00001233334446678800111233344788889
  # 14 | 00134448881223589
  # 16 | 014466389
  # 18 | 0945578888
  # 20 | 22347702
  # 22 | 246999
  # 24 | 09457
  # 26 | 44
  # 28 | 6
  # 30 |
  # 32 |
  # 34 | 9
  # 36 |
  # 38 |
  # 40 |
  # 42 |
  # 44 |
  # 46 | 9
  #
# }
# NOT RUN {
# }