It is difficult to find productive ways to introduce undergraduate students in biochemistry courses to state-of-the-art technologies. The PSAFE project is focused on this goal. Since Fall 2010, students in BIOL 5010 and CHEM 4410 (both biochemistry lecture courses) have undertaken special semester-long projects that introduce them to high-end software for molecular modeling of proteins and nucleic acid-protein complexes. Students are assigned a specific protein (different for each student) that becomes their object of study and interest for the semester. Since 2010, more than 700 students in these two courses have successfully completed a PSAFE project, with approximately 250 more to come in each future year. The complete collection of PSAFE projects is now archived in UVaCollab and available on the Web. In this presentation Professor Grisham will give an overview of the course and his use of UVaCollab for archiving and showcasing student work.

1. PSAFE
Protein Structure And Function Exploration
for Undergraduate Biochemistry Students

2. The Goals
• Expand access to computational tools for UVA
students
• Introduce undergraduate students to state-of-the-art
molecular modeling software
• Encourage students to think critically, creatively and
independently about biochemical research
• Showcase the work of undergraduates within UVA
and beyond

3. Key Contributors
• Reg Garrett, Professor of Biology
• Elizabeth Magnotti, B.S. Chem, UVa, 2011
• Amanda Mullen, B.S. Chem, UVa, 2012
• Erna Kukic, B.S. Chem, UVa, 2013
• Sarah Smith, B.S. Chem, B.A. Biol, UVa, 2014
• Yitna Firdyiwek, Instructional Technology Advisor, ITS

4. The PSAFE Project
• PSAFE is a part of BIOL 5010 and CHEM 4410, both
biochemistry lecture courses
• Each student is assigned a biomolecular structure
• For a semester-long project, done outside of class
• The structure is typically a protein, but sometimes a nucleic
acid or a protein-nucleic acid complex
• Students study their structures all semester and become
intimately acquainted with them
• Final project is a “molecular document” that showcases the
structure and function of their molecular complex and provides
multiple interactive views and animations of the structure

5. Guidance for Students
• A “head TA” is chosen from the previous year’s class
• This TA meets weekly with students to discuss
aspects of the project and advise students
• The head TA also supervises grading of project
milestones
• Students also have access to a library of project
documents online on Collab
• Students also learn to explore a variety of databases
online to learn about their structure

6. The Software
• Molecular documents are created using software
from Molsoft LLC (La Jolla, California)
• Molsoft has graciously provided this sophisticated
software to UVA students and faculty free for 4 years
• The software lets students describe their structure in
text on the left side of the screen
• Hyperlinks in the text control graphic manipulations
on the right side of the screen

7. Archiving the Student Projects
• We are generating 250 projects each year
• Students are eager to preserve and display their work
• Many have asked one and two years later
• Two strategies:
• Cengage (publishers of Biochemistry by Garrett and
Grisham) have placed 140 of the 2010 projects on the
textbook website – an arduous editing project
• We have developed a UVA (Collab) website to display
the collected projects with a shorter turn-around time

8. The PSAFE Website
• The PSAFE website has been built on Collab – the
eventual website will be psafe.us
• The principal challenge has been to transfer so many
projects – 650 now, with many more to come
• Each project consists of several files managed by the
Molsoft software via a home page (which we can call
index.html) and all contained in a folder (directory)
• Yitna Firdyiwek has written a javascript to load the
projects onto Collab
• The script allows projects to be searched according to
student name, protein name, or chapter number

9. How it works
• The folders are named according to the convention:
• ChXX__StudentLastName__FirstInitial__ProteinName, follow
ed in some cases by additional information
• The folder name is decomposed into three parts:
• Chapter number
• Student name
• Protein name
• This allows each project to be listed either by chapter
number, student name or protein name
• The hyperlinked lists that result open the index.html file

10. Thanks to:
• Yitna Firdyiwek
• Sarah Smith and the previous head TAs
• Reg Garrett
• Collab developers and support staff
• Andy Orry, Molsoft LLC and his colleagues
• Our students!