This project was prepared as part of a BioQUEST faculty development workshop entitled Implementing Bioinformatics in Introductory Undergraduate Biology Courses:
Exploring Microbiology, Molecular Data and Visualization
at San Diego Supercomputing Center in January 2007. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

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Molecule Informatics Portfolio
Authors          Audiences          Overview           Materials          Resources           Future Directions



Sandra Slivka
San Diego Miramar College

Guillermina von Borstel
San Diego Unified School District

Tracy Ware
Salem State College


Possible Audiences:

Biology, Biotechnology, or Biochemistry Majors or anyone interested in using informatics tools  


Brief Overview:

Structure Determines Function

Students! Develop a portfolio of structural and functional data on a particular protein that will appear later in this course

As an instructor, you can choose molecules from the Protein Data Bank which allow your students to discover the link between structure and function. An easy & rich source of this information is the archives of 'Molecule of the Month' features on the Protein Data Bank and EMBI sites. As a semester-long project, students expand their portfolio as they learn the informatics tools to access the published data on their protein. When this protein appears within the context of the course, the student acts as an expert to the class by giving a short presentation on the molecule.

Learning Objectives

Students should be able to:
i. Access and interpret structural data about a protein of interest and its homologs
ii. Develop a portfolio of data about the structure and function of their proteins
iii. Serve as an expert source of information when the class encounters this molecule within the class curriculum  


Project Materials:

Physical Protein Model Building Kits. The Amino Acid, Mini Toober, and Water kits are highly recommended.
Protein Data Bank (PDB) Molecule of the Month
EMBI Molecule of the Month
Essential Biochemistry (Pratt and Cornely). Learn to View Protein Secondary Structures
ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.
A Protein Primer with Proteins Set to Music MP3 compatible



- MoleculeInformaticsPortfolio1.doc