Not only proteins or peptides but also low-molecular weight compounds, like calcein.
Depends on what you mean by volume. If you mean hydrodynamic volume, that will include the molecule and whatever water it binds. This is what you would measure using physical techniques such as ultracentrifugation or gel filtration. Often this is expressed as an equivalent sphere, cylinder depending if the shape is roughly spherical, an elongated rigid rod or random coil. I am not familiar with any of the programs mentioned above, but assume they calculate a "dry" volume from the known sizes of various molecular constituents. These will undoubtedly differ from the hydrodynamic volume.
Hi, you can use the VEGA ZZ (http://www.msg.ucsf.edu/local/programs/Vega/pages/gl_info.htm). This program gives you the molecule volume, surface area, polar area and other properties.
Also, there are some approaches to calculate the molecule volume. One of them simulate the atoms like spheres. The van del Waals radio is used to create a set of spheres and the final volume will be calculated through the interception of all volumes.
Hello.
Another program that you may use is MOE (from Chemcomp group). MarvinSketch can also do that for you, but in a less accurate manner.
Best regards.
You can also use the Proshape suite (http://biogeometry.duke.edu/software/proshape/). Open source development by Patrice Koehl, with the only requirements that you should be able to compile fortran and C files.
The program is based on the alpha shape theory and computes *accurately* the surface area as well as volume for the VdW and SA models of any type of molecules.
Mol_Volume from "http://www.ks.uiuc.edu/Development/MDTools/molvolume/" is an other program to look.
Volume of the macro-molecule is calculated by method somewhat similar to Monte Carlo method, namely, by measuring how many vertices of a dense regular grid.
It is free for academic use.
What do you need the answer for? Crystallographers often use a very simple formula: you expect an organic molecule to take up 18 cubic Angstroms per non-hydrogen atom in a crystal. Some people use 20 instead to make calculations even easier.
Many packages mentioned above will be able to give more accurate results, but the use of the added accuracy is questionable. Very small changes in conformation of a molecule or changes in the hydrogen bonds around the molecule, can have surprisingly large effects on the very well defined Voronoi volumes.
Dear Rob, for calcein (C30H26N2O13) we obtain two estimates of 810 or 900 cubic Angstroms, if we assume density of 18 or 20 A3/non-hydrogen atom. For bigger molecules the difference may have no sense. But for small molecules, probably, it is better to use 18 A3/non-hydrogen atom to obtain a more realistic value. Am I right?
Peter, Calcein has a molecular mass of 623 gram/mole, and its massive aromatic part gives it a relatively high density of 1.75 gram/cm3. This comes to a volume of 356 cm3/mole or around 600 cubic Angstroms per molecule. I think this formula will be more accurate than this for most molecules but this gives you a good idea of what you can get with such a simple formula.
Depends on what you mean by volume. If you mean hydrodynamic volume, that will include the molecule and whatever water it binds. This is what you would measure using physical techniques such as ultracentrifugation or gel filtration. Often this is expressed as an equivalent sphere, cylinder depending if the shape is roughly spherical, an elongated rigid rod or random coil. I am not familiar with any of the programs mentioned above, but assume they calculate a "dry" volume from the known sizes of various molecular constituents. These will undoubtedly differ from the hydrodynamic volume.
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