SURFace Algorithms

SURFace algorithms are programs that calculate solvent accessible surface area and curvature corrected solvent accessible surface area. The accessible surface output is calculated for the whole molecule, per residue, and per atom. SURFV calculates solvent accessible area which is defined by a probe as it rolls on the surface of the molecule. Thus use of a zero radius probe will give the Van der Waals surface area. SURFCV calculates solvent accessible area and an average curvature.

The surface area in both programs is determined in terms of Lee & Richard (rolling probe) method. The accessible surface output is calculated for the whole molecule, per residue, and per atom allowing detailed analysis.

Downloads

Click here to download SURFace Algorithms.

Click here to access sample size files.

System requirements

SURFace algorithms run on SGI and linux systems.

No windows OS version available.

Using SURFace algorithms

README for SURFV:

surfv calculates solvent accessible area which is defined by a probe as it
rolls on the surface of the molecule. Thus use of a zero radius probe will
give the Van der Walls surface area.

makefile is for an SGI system. For others make your own.

It is executed by a single command line as in

surfv (resolution) (probe radius) (sizefile) (pdbfile) 1(0) 1(0) 1(0)

where

resolution indicates the fineness of the mesh generated on the template sphere.
It takes on integer values 1 - 4 with 4 giving the finest mesh. Usually a
value of 2 or 3 will suffice

1 - 122 points on the template sphere
2 - 482
3 - 1922
4 - 7682

probe radius is usually assigned a value of 1.4A which is often used in
rendering molecular surfaces

sizefile gives the radii of atoms; it has to be in a specific format (see
def.siz for format)

pdbfile is the standard brookhaven file giving the cartesian coordinates of
atoms

The last 3 parameters add additional features to the program.

A non-zero integer in the 5th field will print out the residue areas in file
pdbfile.res. Likewise a non-zero integer in the 6th field will write out atomic
areas in pdbfile.atm

By default surfv will ignore hydrogens in area calculations even if there is
an entry for them in the size file. You can override this option by using a
non-zero integer in the 7th field of the input line

The atm and res files are in multi-column format. If you want single column
format output (if you need to use this output in your script) then invoke
surfv with an -s option as in

surfv -s (nlevel) .......

README for SURFCV:

surfcv calculates solvent accessible area and an average curvature (see
nicholls, sharp and Honig PROTEINS,11,p 281 (1991)

It is executed by a single command line as in

surfcv (resolution) (probe radius) (sizefile) (pdbfile) 1(0) 1(0) 1(0)

where

resolution indicates the fineness of the mesh generated on the template sphere.
It takes on integer values 1 - 4 with 4 giving the finest mesh. Usually a
value of 2 or 3 will suffice

probe radius is usually assigned a value of 1.4A which is often used in
rendering molecular surfaces

sizefile gives the radii of atoms; it has to be in a specific format (see
def.siz for format)

pdbfile is the standard brookhaven file giving the cartesian coordinates of
atoms

The last 3 parameters add additional features to the program.

A non-zero integer in the 5th field will print out the residue areas and
curvatures in file fort.7. Likewise a non-zero integer in the 6th field will
write out atomic areas and curvatures in fort.8

By default surfcv will ignore hydrogens in area calculations even if there is
an entry for them in the size file. You can override this option by using a
non-zero integer in the 7th field of the input line.

References

Nicholls A, Sharp KA, Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991;11(4):281-96.

Sridharan S, Nicholls A, Honig B. A new vertex algorithm to calculate solvent accessible surface areas. Biophys J. 1992;61:995.

Acknowledgments

SURFace Algorithms is supported by a funding from the National Science Foundation Grant # DBI-9904841.

Developed in the Honig Lab.

Questions

For questions related to SURFace Algorithms, please contact honig_software@c2b2.columbia.edu.