Bio 28 – (Next Session: Spring 2018)
Welcome to the “Introduction to Bioinformatics” page. In this class, you will explore several bioinformatics tools and databases, and their use in the modern molecular biology research. We will focus on the molecular and structural bioinformatics. Several topics discussed in this class includes: molecular genetics, structural biology, sequence alignment, genome structure, protein evolution, molecular docking, and advanced topics (drugs discovery, protein engineering, or system biology). Curiosity and enthusiasm for learning are the only pre-requisites for this class, although background in basic molecular biology certainly helps.
Class meets every Tuesday & Thursday 9:30 am – 11:55 am
Recommended textbook for the course:
- Primary – Introduction to Bioinformatics, by Arthur M. Lesk
ISBN-13: 978-0199651566 ISBN-10: 0199651566
- Others – text in general biology (Campbell)
Below are some activities that we did last year, and molecular artwork of some of the students (Spring 2017). Contact me (akamajaya@pasadena.edu) if you have any further question regarding the class.
Caltech Tour – May 24, 2017
Anand Muthusamy discussed several computational tool in protein chemistry research, including molecular dynamics, FRET, and bioorthogonal chemistry. Afterward, we visit the Lester lab to watch a demo from Dr. Nichols on protein biosensor engineering. Cool stuff!!!
Our Sp 2017 Bioinformatics group – In front of the famous turtle pond, Caltech
Here are several cool molecular artwork from the students in Spring 2017 Bioinformatics class @PCClancer
Illustration of S. pyogenes Cas9 in complex with single guide RNA (sgRNA) and its target DNA. The groove between the recognition (REC) lobe (dark blue) and nuclease (NUC) lobe (cyan) is positively charged, allowing the target sgRNA (burgundy)-target DNA (yellow) heteroduplex to nestle into the structure. Notice the T-shaped structure consisting of the sgRNA:target DNA duplex and the stem loops 1-3 (purple). PDB ID: 4OO8
– Work by Veronica G Guizar
In the figure above, a model of the CRISPR-associated endonuclease (Cas9) protein was modified to show only the recognition (REC) lobes, the PAM-interacting (PI) domain, and the guide RNA-target DNA heteroduplex. The REC lobes include the REC1 (plum pink) & REC2 (coral orange) domains. The PI domain (pink) is at the bottom of the figure. Target DNA (yellow) & the single guide RNA (sgRNA) interact via watson-crick basepair interaction.
– Work by Dan B Vuong
PFR = Perforin
– Work by Veronica Guizar
Superposition of myoglobin structure (cyan, PDB ID 1MBO) with one subunit of hemoglobin (gray, PDB ID 2HHB). This animation highlight the interaction between the proximal histidine (myoglobin = magenta, hemoglobin = blue), the porphyrin ring (shown in stick representation), and the oxygen molecule (red).
– Work by Jennifer Shintaku (@J_Shintaku)