Charles M. Grisham: Protein Structure and Function Explorations (PSAFE): Showcasing Molecular...
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Transcript of Charles M. Grisham: Protein Structure and Function Explorations (PSAFE): Showcasing Molecular...
PSAFEProtein Structure And Function Exploration
for Undergraduate Biochemistry Students
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
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
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
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
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
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
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
How it works
• The folders are named according to the convention:
• ChXX__StudentLastName__FirstInitial__ProteinName, followed 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
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!