Graduate Project


Protein geometry and conformation resource database Public Deposited

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  • This project is about helping protein naturalists understand the protein structure. The database system developed here provides a convenient tool for scientists to explore conformational information in a database of known structures and thereby provide researchers with a deeper and wider view of the empirical data. In this way, it will aid the scientists in their research to understand the rules and principles concerning protein folding and stability. The flexible, updateable, dynamic, and user-friendly features of the system will allow it to be a powerful tool that provides accurate, specific, and detailed information based on user's input. This system implemented important functions in PHP to support the sub­query of any possible combinations of parameters involved for residues of different position combinations, which makes it possible for the users to define specific parameters for up to pentapeptide residues stretches. Local geometry* and conformational distribution plots, statistical analyses and parameter summary tables of any combinations of the geometric parameters can be generated dynamically based on search results. A smoothing function* can be applied to improve the statistics by increasing the numbers of observations within each observational unit. The dynamic query results can be exported for further statistical analysis in EXCEL and other programs. This database system is implemented in PHP/mySql and is a free resource that is easy to maintain.
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