This two-page paper is to discuss the class project on the effective ways to calculate and render molecular surface; my contribution to the research, and far as my web page is concerned; and the contribution of the entire class, as depicted by the project web page.

The Project: Idea The basic idea behind this research project is to research and analyze various molecular surface computation techniques, and come to a convincing conclusion as to which technique is most effective, considering factors like time and structure of the computation. Our conclusion will be complete and in the form of a paper, for publishing by reputable scientific journals and magazines.

Why We chose to research on molecular graphics since it forms part of a very important field of scientific research. Chemical formulae of molecules and compounds do provide chemists with a fair idea as to what kind of molecule it is, and how it may be compounded with other molecules in the development of a drug. However, this leaves much to be desired since the chemist is not only interested in the atoms or elements constituting the molecule (as is the information provided by the molecular formula), but rather, more interested in how these atoms are bonded with each other. In computing the molecular surface, we are able to generate a structure of the molecule, thus providing the chemist with a very fair idea about the structural formula of the molecule and hence knowledge about how the atoms constituting it are bonded together. Thus in choosing this project, we chose to identify and compare all or most of the possible techniques there are to compute molecular surfaces, and which, if any, provides the most accurate information about a molecule, within a fair amount of time.

Process A molecule is made up of a complex structural arrangement of bonded atoms in space; somewhat related to points in a 3-dimensional space for which a Voronoi diagram is constructed. Thus we began our project by analyzing concept behind Voronoi diagrams and Delaunay triangulations for points in three-dimensional space. We then went on to discuss and test algorithms to perform computations for these two concepts, thus building a foundation for understanding how molecular surfaces may be computed.

At Present Presently, we as a class have researched various molecular surface calculation algorithms and software, which we are using to test a selected set of input data from the Protein Data Bank. We compare our results, and try to identify which software or algorithm is most effective, especially as far as time complexity is concerned.

Overheads and Solutions We realized that each these algorithms or software were designed to provide certain information about the molecular surface, which may or may not be evident in the computation of other software or algorithms of the same surface. Thus, for uniformity sake, and to get the best comparisons as possible, we resorted to specify a few details as to what we expected of each algorithm. These specifications included: using a uniform probe radius, uniform atomic radii specification, noting the number of atoms (all) whose surface is being computed, area of the surface being computed (van-der-waals surface), and time taken for computation.

Sources Information for this research project has come from very good journals, scientific and mathematical research websites, the required texts (I. Valiela, "Doing Science: Design, Analysis and Communication of Scientific Research", and E. Tufte, "The Visual Display of Scientific Information, 2nd ed."), as well as other text.

My Web Page The purpose of my creating my own web page for this class is to enable me put my findings online for others to see my performance and progress, thereby fostering a healthy comparison and exchange of ideas, which invariably leads to better my understanding of the concept of molecular graphics.

The Project Web Page The purpose of the project web page is to provide a common ground or platform where all the information gathered my the class so far, can be placed, to encourage and expedite comparison and well as discussions on the various issues encountered during the course of the project. It also acts as the main resource for our future publication, and hence requires us to input all relevant data there.

Conclusion On the whole, the project has demanded a lot of research, analysis and testing time from each student in the class. We have learnt the art of good experimentation; and effective ways of data representation, especially as far as graphing is concerned. And we hope to use what we have already obtained, to attain our main objective for this project. http://www.sb.fsu.edu/~chapman/Home/Publications/Chapman_&_Connolly_International_Tables_1999/Molecular_Surface_Calculations.html