ASAB1

Having acquired the appropriate PDB files, it is necessary to tag each residue as being either a surface side chain or main chain residue, or a buried residue. Arbitrary numerical codes are assigned by the program to each residue component i.e. 1 for surface side or main chain, 6 for buried surface side chain, and 10 for buried main chain. The program is based on Lee and Richards' (1971) rolling sphere algorithm to determine surface accessibility. The steps required to run ASAB1 are listed below.

Prepare the PDB file: ASAB1 only processes information specified in the ATOM and HETATM fields of the PDB file, terminating at the TER field. Therefore it is preferable (but usually not necessary) to remove additional information prior to running ASAB1, while it is mandatory to remove any intermediate TER field for proteins containing multiple chains, otherwise ASAB1 will terminate execution prematurely.

Running the program

Launch asab1 at the command line. Supply information for the size of the rolling sphere probe as requested by the program. A typical run would use a rolling sphere with 1.4 Å radius Enter the threshold value for surface accessibility (usualy 10 Å^2). Insert PDB filename (complete with extension). Choose between standard output filenames or enter root filename. The three standard output files generated by the program are named provaly, provaly1 and provaly2, which contain the atomic coordinates; atomic radius, mass and surface accessibility code; and correspondence i.e. atom name, residue name and residue name and number. Enter the integration step (usually 1 Å). The number of steps appears, confirm to start operation. ASAB1 can also be used to calculate the surface accessibility of bead models (option 3 - recheck), which requires a percentage value for the surface threshold. This is essentially a ratio of exposed surface area/total surface area for each bead. For example, if a value of 50% is used, then the rolling sphere has to cover at least half the area of the sphere for it to be tagged as being surface accessible. Therefore higher percentage values will result in a greater number of buried beads. This feature is used to recompute the surface accessible beads after SOMO generation. By using only the surface accessible beads in the computation, the hydrodynamic parameters for the model can be calculated much more quickly. This should not be confused with a shell model just because it does not include 'buried' beads. In shell models the beads are much smaller and they are more closely packed along the surface. In fact, these medium-resolution models lie somewhat between shell and low resolution bead models (several residues per bead), and completely excluding the buried beads from the computations may lead to some errors.