Justin Miller awarded a Dissertation Year Fellowship
Justin is a 4th year PhD Student in the Molecular Biology Institute researching in the laboratory of Dr. Todd Yeates. His research work is focused on applying synthetic biology principles and computational methods to design therapeutic proteins and therapeutic delivery vectors. As an undergraduate student at UCLA, Justin studied Microbiology, Immunology & Molecular Genetics. Now at TDG, he works primarily with biologics, where he draws from his background in molecular and structural biology to better understand details of university-generated inventions.
SAVES
Structure Analysis and Validation
SAVES has been in operation since 2004 and is currently operating version 6. It is an interactive validation server for 5 programs commonly used in protein structure validation. Some of these tools were initially invented in the early 1990s in FORTRAN code and some have been upgraded to be in C++ code. Some of them have source code available. All of them can be run through the dashboard screen concurrently and results can be downloaded for later use.
The server runs between 1,000 and 2,000 jobs every day from users around the world. Due to this, we only hold on to a job’s results files for 1 week. However, it is always easy to run a job again. And you don’t have to run them all, pick any program to run on its own using the same dashboard.
References
ERRAT
- Reference: Verification of protein structures: patterns of nonbonded atomic interactions, Colovos C and Yeates TO, 1993.
- C++ software
VERIFY 3D
- Profile Search Software [Bowie et al., 1991, Luethy et al., 1992].
- DSSP original and Wikipedia
PROVE
PROCHECK
WHATCHECK
- WHATCHECK documentation and source
For questions about WHATCHECK results, please email the creator: vriendgert@gmail.com
