A molecular simulation study of the utility of methyl groups as probes of protein packing and flexibility and maintaining the computational environment for computational biomolecular research

Document Type



Master of Science (MS)


Computer Science

First Advisor's Name

Shu-Ching Chen

First Advisor's Committee Title

Co-Committee Chair

Second Advisor's Name

David Chatfield

Second Advisor's Committee Title

Co-Committee Chair

Third Advisor's Name

Giri Narasimhan

Date of Defense



Methyl groups are ubiquitous in proteins and may be useful probes of protein packing and flexibility. The purpose of this research is to determine a practical computational method for predicting methyl group dynamics and to determine its correlation with protein packing and flexibility. Molecular dynamics simulations were performed on a set of four crystalline amino acids and peptides (Ala, Leu, Val, and CLA) and the proteins staphylococcal nuclease (SNase) and HIV-1 protease. The dynamics of methyl rotation was quantified and compared with the results of NMR experiments and rotational barrier calculations.

This study required considerable computational resources, and hence the setup and maintenance of the computational environment is an important aspect of the research. Installation of hardware and software, customization of software, maintenance of user accounts, and the writing of scripts to optimize use of the computer resources was required.



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