How DMS Computes the Molecular Surface of a Molecule

DMS (Distributed Molecular Surface) is a software program that calculates the molecular surface of a molecule. The molecular surface resembles the van der Waals surface of a molecule, except that crevices between atoms are smoothed over and interstices too small to accommodate the probe are eliminated. The surface includes cavities in the interior of the molecule, even if they are not accessible to a solvent molecule coming from the outside.

The molecular surface calculated is that defined by F. M. Richards (1977, Ann. Rev. Biophys. Bioeng. ). In particular, the calculated molecular surface is that traced out by the surface of the probe sphere rather that the probe sphere's center. According to Richards' definition the molecular surface consists of two parts: contact surface and reentrant surface. The contact surface is made up of ``those parts of the molecular van der Waals surface that can actually be in contact with the surface of the probe.'' The reentrant surface is defined by ``the interior-facing part of the probe when it is simultaneously in contact with more than one atom.'' Dms reports the amounts of contact and reentrant surface area, and the combined total surface area on the standard error output

DMS has the advantage to run on multiple machines or servers simultaneously. Thus, on the start of the program, all neighbor information is sent to all available servers, and then proceeds to compute the molecular surface.

The Computation:

• Assign a radius for each atom
• Gets the radii list and assign the Van der Waal’s radius for each atom.

• Compare and sort the atoms by coordinate so we can look just at slices instead of all atoms when looking for neighbors

• Start up servers on all the machines that we can reach and hand them the necessary parameters as well as atomic coordinates

• Loop through the atom list and assign selected atoms to available servers (this produces a list of neighbors).

• Neighbor information is then passed to all the compute servers in preparation for surface computation.

• Loop through the neighbor list and ask for probes, which contact both neighbors simultaneously. The probe information is then passed to all the compute servers as well.

• Now all neighbor info is cleaned up the and sent out again

• Generate surface points; First the contact, then the toroid reentrant, and finally spherical reentrant

• Collapse near-coincident probes (remove redundant surface coverage) and then compute surface area

• DONE!!