Calculations of protein volumes: sensitivity analysis and parameter database

Motivation: The precise sizes of protein atoms in terms of occupied packing volume are of great importance. We have previously presented standard volumes for protein residues based on calculations with Voronoi-like polyhedra. To understand the applicability and limitations of our set, we investigated, in detail, the sensitivity of the volume calculations to a number of factors: (i) the van der Waals radii set, (ii) the criteria for including buried atoms in the calculations or atom selection, (iii) the method of positioning the dividing plane in polyhedra construction, and (iv) the set of structures used in the averaging. Results: We find that different radii sets have only moderate affects to the distribution and mean of volumes. Atom selection and dividing plane methods cause larger changes in protein atoms volumes. More significantly, we show how the variation in volumes appears to be clearly related to the quality of the structures analyzed, with higher quality structures giving consistently smaller average volumes with less variance. Availability/Supplementary Information: Programs and associated data files are available from http://bioinfo.mbb.yale.edu/geometry and http://molmovdb.org. In particular, we make available an extensive database of many different sets of protein geometric parameters. Contact: JerryTsai@TAMU.edu; Mark.Gerstein@Yale.edu * To whom correspondence should be addressed.