Structural Analysis and Modeling of Proteins on the Web: An Investigation for Biochemistry Undergraduates

Teaching computer analysis and modeling of proteins at undergraduate universities can prepare students for their anticipated careers as future biochemists. Although there are a variety of software packages that researchers use for structural analyses of protein and nucleic acid sequences, these packages may be too complicated for undergraduates to learn within a few weeks, or they require an expensive graphics workstation to be useful. One manner to overcome such limitations is to access databases and structural analytical tools via the World Wide Web (WWW). This approach was used successfully in teaching an advanced biochemistry course (protein structure and folding) and was investigated further as an undergraduate research project. Presented here is the method used and an example where a student predicted the tertiary structure of a fragment from a DNA-binding protein after first acquiring the skills necessary to utilize the information from the Internet. This paper documents that undergraduates who do ...