CSC 181 - Advanced Research Topics in Computer Science

The goal of this project is to compare algorithms for computing molecular surfaces and to make a prediction as to what the best strategy for such computation is. A molecular surface (MS) is defined by Lee and Richards [1971 ref.] as the surface resulting from rolling a probe sphere on the van der Waals surface. The MS, also known as the solvent-excluded surface, is traced by the portion of the probe sphere surface facing the van der Waals surface. Another definition used in the literature is the solvent-accessible surface, which is traced by the center of the probe sphere

The following algorithms are being considered:

	CSC 181 - Advanced Research Topics in Computer Science
	The goal of this project is to compare algorithms for computing molecular surfaces and to make a prediction as to what the best strategy for such computation is. A molecular surface (MS) is defined by Lee and Richards [1971 ref.] as the surface resulting from rolling a probe sphere on the van der Waals surface. The MS, also known as the solvent-excluded surface, is traced by the portion of the probe sphere surface facing the van der Waals surface. Another definition used in the literature is the solvent-accessible surface, which is traced by the center of the probe sphere The following algorithms are being considered: Double cubing lattice method [Eisenhaber 1995] Smooth Invariant Molecular Surface (SIMS) [Vorobjev 1997] Distributed Molecular Surface (DMS) [Huang 2002] Improved Solvent-excluded Molecular Surface Area Using Boolean Masks [Bystroff 2001] Michel Sanner's algorithm (MSMS) [Sanner 1995] Alessandro Pedretti's (VEGA) [A. Pedretti, L. Villa, G. Vistoli 2002]
	Professor Herbert J. Bernstein email(yaya@bernstein-plus-sons.com)
	Project Participants Rohit's CSC 181 Page Performance analysis of Delaunay Tree 3, and VEGA Petko Ivanov's CSC 181 Web Page Vencislav Stanev email(kokobokov@hotmail.com) Parag Jain's webpage for CSC 181 Peter Zhivkov (page presents SIMS [Vorobjev 1997] and QHULL) Daniel's Webpage
	Input Specification
	Output comarison
	Bibliography
	PDF of paper submitted to NCUR 2003
	Evolving Draft Paper
	Raw Data (Excel)
	Comparable Data (Excel)
	NCUR Pictures
	Final Presentations MASKER - Parag Jain
	News 12/6/02 Herbert Links added for data spreadsheets 11/22/02 Herbert Link added for draft paper. Be sure to keep the link if you change the page 11/21/02 Vince I have just changed the layout of the page as you may notice. Please if any of you have any concerns or simply likes the old version better go to directory backup and resotore it. If you have useful suggestions feel free to contact me.

Project Participants

Final Presentations

News