Seminars

The workshop will consist of two parts. In the first part, we will cover fundamental topics in structural bioinformatics. The topics include:

•    Protein structure and sequence databases
•    How can we manage such large data?
•    Clustering
•    Multiple sequence alignment
•    Protein Structure (in multiple sequence alignment)1
•    Predicting protein structure (Protein folding problem)
•    Statistics-based potential
•    Amino acid exchange matrix
•    Intrinsic disorder
•    RNA structure and function2


In the second part of the workshop, we will show how our structural bioinformatics methods have been successfully applied in biological research. Applications here include:

•    Structural modeling of Regnase-1 (zc3h12a) and docking to mRNA targets
•    Structural modeling of arid5a and docking of mRNA targets3
•    Modeling of whole dengue virus and docking to neutralizing antibody
•    Engineering of a high affinity antibody-peptide complex (pa-tag system) Structural modeling and docking of the TLR adaptor molecules TRAM/TRIF 4

References
1.    Katoh, K. & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30, 772-80.
2.    Li, S., Karlou Mar, A., Yamashita, K. & Standley, D. M. (2014). Quantifying sequence and structural features of protein-RNA interactions. Nucleic Acids Research accepted.
3.    Matsushita, K., Takeuchi, O., Standley, D. M., Kumagai, Y., Kawagoe, T., Miyake, T., Satoh, T., Kato, H., Tsujimura, T., Nakamura, H. & Akira, S. (2009). Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Nature 458, 1185-90.
4.    Enokizono, Y., Kumeta, H., Funami, K., Horiuchi, M., Sarmiento, J., Yamashita, K., Standley, D. M., Matsumoto, M., Seya, T. & Inagaki, F. (2013). Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling. Proc Natl Acad Sci U S A 110, 19908-13.