[MMTK] Finding accessible surface area of atoms/residues in proteins

Peter peter at maubp.freeserve.co.uk
Mon Nov 8 14:17:13 CET 2004


Hello,

I was wondering if anyone has tried to use MMTK to calculate the (solvent) accessible surface area of atoms/residues in a protein loaded from a PDB file.

I have seen references to a program called ACCESS:-

Hubbard, S.J. (1991) ACCESS, a Program for Calculating Accessibilities. Department of Biochemistry and Molecular Biology, University College London, London.

I didn't find any mention of this on the UCL website, but it appears to have been superseded by Naccess:-

Hubbard, S.J. & Thornton, J.M. (1993), 'NACCESS', Computer Program, Department of  Biochemistry and Molecular Biology, University College London.

http://wolf.bms.umist.ac.uk/naccess/

NACCESS implements the Lee & Richards method in Fortran 77:-

B. Lee and F. M. Richards (1971), The interpretation of protein structures: Estimation of static accessibility, Journal of Molecular Biology 55 (3), 379-380.

Perhaps something similar could be done using MMTK...

Thank you

Peter

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