I want to find the accessible surface area and the volume of a protein, giving PDB file as the input for the protein. I used two servers, 3vee and Vadar. For the PDB id, 1LTM, the websites are giving me different volume and surface area measures as follows:

3vee (vol: 50951 A^3; Surface area: 10837 A^2)
Vadar(vol: 40937.8 A^3; Surface area: 14680.6 A^2)

Can anyone tell me which server to use, which server is more accurate? If you know of any other server giving accurate result, please let me know that too.


Note: Both the publications are from Nucleic Acids Research, I guess I do not need to validate them. 3vee has been published in 2010 with citation of 164 and Vadar was published in 2003 with citations of 416. Is it okay if I take 3vee since it is the latest tool?

  • How big is the protein/complex? Can you download something like UCSF Chimera or Pymol and calculate it yourself to see if it agrees with either of those numbers? You may also want to check that the surface calculation parameters in both programs are using a similar probe radius. I'd guess from the fact that Vadar has a smaller volume but greater surface area, that it's probe diameter is smaller. – Joe Healey Sep 27 '16 at 9:31
up vote 1 down vote accepted

You can use PDBSum and PDBe-PISA servers for calculating accessible surface area and buried surface area and Castp server for finding pockets within your protein molecule. If your protein is globular, you can measure the diameter in pymol and calculate its volume. Hope it helps.

  • can you add some references and/or links so that others who are less familiar with your answer and the question can follow along? it would definitely strengthen your answer – Vance L Albaugh Dec 18 '16 at 1:54

The results depend on the atomic radii and on the probe radii. Without them, it is impossible to have an opinion about the volumes and surfaces values.

Using C=1.75, N=1.55, O=1.4, S=1.8, and adding 1.4 for the probe, running the Monte-Carlo method interactively available in ASV outputs for 10000000 random points (only ATOM records were input): V = 57335.548996 +/- 1.96*34.439 ; S = 14887.818374 +/- 1.96*20.345

You can download ASV from: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html ; No installation procedure is required, just flag the binary as executable with the chmod command. Monte-Carlo f77 source routines are supplied too.

References:
M. Petitjean, J. Comput. Chem. 1994, 15[5], 507-523;
M. Petitjean, Spheres Unions and Intersections and Some of their Applications in Molecular Modeling. In: Distance Geometry: Theory, Methods, and Applications, chap.4, pp.61-83, Springer, 2013.

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