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Publication Date


Document Type

Honors Project


Computer Science


Protein folding-Computer simulation, Proteins-Conformation, Proteins, Ph, Conformational change, Protein flexibility, Rigidity, Survey, Software


Proteins are chains of amino acids that are folded into 3D structures. A protein can be rep- resented as a graph, where the atoms are vertices, and the bonds and various electrostatic interactions between the atoms are edges. The rigidity and exibility of this structure can be analyzed with the software FIRST, developed in Mike Thorpe's Laboratory at Arizona State University. KINARI, a software package that is being developed at the LinKaGe Lab at Smith College and the University of Massachusetts, Amherst, for protein rigidity and exibility analysis, will o er more features than FIRST. So far, most of the studies using FIRST have been done on a small group of proteins. The aim of this study is to develop a software infrastructure that would allow researchers to perform automated rigidity and ex- ibility computer experiments on many proteins. A literature survey of most studies using FIRST was performed in order to understand what pre-processing is done by researchers and what measures of rigidity should be collected. Using this information a software in- frastructure in Ruby and R was implemented. This infrastructure allows a user to input a list of Protein Data Bank (PDB) les in several ways (as a list, a Structural Classi cation of Proteins (SCOP) family id) and then automatically downloads those les. Then it runs KINARI on all of the les, reports if execution on some particular les failed, aggregates results, and collects statistics. It works both as a stand-alone command-line version and as a web server. It can perform surveys on the whole PDB. Additionally, experiments were devised to explore how rigidity is related to pH dependent conformational changes of the SARS Coronavirus Main proteinase protein. i




iii, 69 p. : col. ill. Honors Project-Smith College, Northampton, Mass., 2010. Includes bibliographical references (p. 60-64)