Automatic identification of protein domains
Steven Brenner, Professor
Plant and Microbial Biology
Applications for Spring 2025 are closed for this project.
Proteins often fold into compact structural units, called domains. Protein domains are basic units of protein function and evolution. Delineating domain boundaries is a prerequisite for further analyses of protein structures. However, this process is largely a manual process and the accuracy of these computer programs is still not satisfactory. This project will include two parts: critical assessment of current protein domain identification programs, and development of approaches to improve the accuracy by combining existing computer programs. Students interested in AJAX web development are also invited to help improve the web interface for displaying current data on protein domain architectures.
Qualifications: The ideal candidate is willing to learn and knows how to write programs (in any language); knowledge of protein structures is a plus. Applicants with GPA under 3.6 will be considered only in exceptional circumstances.
Other requirements: Candidates must:
•Attend 3-hour lab meeting every week
•Attend personal genomics subgroup meeting every week
•Adhere to all lab policies (including weekly notebooks to track research, semester reports)
•Must register for credits, regardless of program-specific requirements.
Day-to-day supervisor for this project: John-Marc Chandonia, Staff Researcher
Hours: 9-11 hrs
Related website: http://compbio.berkeley.edu
Biological & Health Sciences Engineering, Design & Technologies