Investigating Rigidity Properties and Atomic Content of Proteins
Document Type
Oral Presentation
Campus where you would like to present
SURC 137B
Start Date
21-5-2015
End Date
21-5-2015
Keywords
Proteins, Rigidity, Scripts
Abstract
Proteins are three-dimensional molecules that bend and flex to perform a multitude of functions, ranging from cellular repair, to mediating the immune response, to aiding in neuronal signal propagation. Drugs are designed to regulate protein functions and their interactions, which they do by closely associating with cavities or other structurally important features on a protein’s surface. Because the properties of protein cavities have not been analyzed in a dataset large enough, it is unclear how, or to what extent, the geometric properties and atomic content of a cavity play in facilitating a protein’s interaction with other molecules. Analyzing the rigidity properties and atomic content of protein cavities from a large database would allow development toward a deeper understanding of how proteins interact with other molecules. Preliminary results from a dataset of about 20,000 cavities have already indicated a dominant region for cavity size and the number of rigid clusters within. For our work, we are trying to determine if the molecular content of rigid bodies within cavities can be used to distinguish them from other proteins by using metrics gathered on the size of cavity, the number of atoms in the cavity, and the types of those atoms. To accomplish this, we have created a series of custom BASH scripts to calculate metrics based on information gathered from calculated cavity data and the biological data of the protein.
Recommended Citation
Walling, Christian, "Investigating Rigidity Properties and Atomic Content of Proteins" (2015). Symposium Of University Research and Creative Expression (SOURCE). 43.
https://digitalcommons.cwu.edu/source/2015/oralpresentations/43
Department/Program
Computer Science
Additional Mentoring Department
Computer Science
Investigating Rigidity Properties and Atomic Content of Proteins
SURC 137B
Proteins are three-dimensional molecules that bend and flex to perform a multitude of functions, ranging from cellular repair, to mediating the immune response, to aiding in neuronal signal propagation. Drugs are designed to regulate protein functions and their interactions, which they do by closely associating with cavities or other structurally important features on a protein’s surface. Because the properties of protein cavities have not been analyzed in a dataset large enough, it is unclear how, or to what extent, the geometric properties and atomic content of a cavity play in facilitating a protein’s interaction with other molecules. Analyzing the rigidity properties and atomic content of protein cavities from a large database would allow development toward a deeper understanding of how proteins interact with other molecules. Preliminary results from a dataset of about 20,000 cavities have already indicated a dominant region for cavity size and the number of rigid clusters within. For our work, we are trying to determine if the molecular content of rigid bodies within cavities can be used to distinguish them from other proteins by using metrics gathered on the size of cavity, the number of atoms in the cavity, and the types of those atoms. To accomplish this, we have created a series of custom BASH scripts to calculate metrics based on information gathered from calculated cavity data and the biological data of the protein.
Faculty Mentor(s)
Filip Jagodzinski