Dr. Kevin Shaw
100 Campus DR, #3097
Grove City College
Grove City, PA 16127-2104
Proteins are synthesized by ribosomes as a linear sequence of amino acids. The sequence of amino acids in a protein is reflective of the gene sequence that codes for the protein. Beyond the genetic information, the primary structure holds all the information necessary for a protein to fold into an intricate, three-dimensional structure. This three-dimensional structure is the active, functional protein structure. Unlike the genetic code, the "rules" for protein folding are not fully understood.
I am interested in determining the magnitude of the molecular forces that favor the folded protein over the unfolded protein. I am also interested in using an understanding of these forces to increase the folding energy of medically or industrially important proteins. I am also interested in developing and using computational algorithms for protein design.
gfp is get from PDB (the Protein Data Bank). This program retrieves coordinate files from the wwPDB repository of your choice. By default gfp reads from and writes to STDIO allowing gfp to because part of a larger pipeline. gfp also does exceptionally well in downloading large numbers of PDB files in a single operation. gfp requires a functioning Perl, Wget and Gzip. gfp is licensed under the GPLv2, and gfp is available here.
Retrieve my protein thermodynamic data from the ProTherm Database.
A large compilation of amino acid pK values are available in both human and machine readable form.
A good list of research tools can be found at Pedro's BioMolecular Research Tools.
If you are interested in very large prime numbers, or distributed computing projects in general, visit the Great Internet Mersenne Prime Search.
Need help typesetting with the TeX system? Try the TeX Users Group website.