Compact course: Structural Bioinformatics

Dr. Bingding Huang

This 3-day compact course will provide the participants an overview on structural bioinformatics, especially on computational algorithms to analysize protein structures. In the first day, I will give an introduction to protein structure, followed by fundamental algorithms to align protein sequences. In the second day, I will continue the algorithms for structure alignment and clustering. Two structural databases (SCOP and CATH) will also be descriped. The pratical exercises will be provided to the participants to help them enhance the understanding on the concepts of algorithms. In the last day, I will talk about my recent research on protein binding site prediction and protein-protein docking.

Detailed schedule:
Day 1 (30.11): Introduction to protein structure (PDB), sequence aligment (Dynamic programming, Blast algorithm) and practical exercise
Day 2 (01.12): Structure alignment (superposition), clustering algorithm, SCOP and CATH database and practical exercise
Day 3 (02.12): Lecture: Protein binding site pediction (metaPocket, metaPPI), Protein-protein docking (BDOCK, SDAC)

Books:

• Structural Bioinformatics, Editors: Phil Bourne and Helge Weissig, link
• Structural Bioinformatics: An Algorithmic Approach, Forbes Burkowski, University of Waterloo, Canada, link
• Introduction to Bioinformatics, A. Lesk, Chapter 4 and 5. Oxford University Press, 2002, link

References:

• Bioinformatics lectures given by Prof. Michael Schroeder at TU Dresden, link.
• Bingding Huang (2009), metaPocket: a meta approach to improve protein ligand binding site prediction , Omics, 13(4), 325-330. webserver, pdf.
• Domantas Motiejunas, Razif R. Gabdoulline, Ting Wang, Anna Feldman-Salit, Tim Johann, Peter J. Winn, Rebecca C. Wade. Protein-protein docking by simulating the process of association subject to biochemical constraints. Proteins (2008) 71, 1955-1969. link
• Bingding Huang and Michael Schroeder(2008), Using protein binding site to improve protein-protein docking, Gene, Epub 1;422(1-2):14-21. webserver, pdf
  
• Bingding Huang and Michael Schroeder (2006), LIGSITE^csc: predicting protein binding sites using the Connolly surface and degree of conservation, BMC Structural Biology, 6:19. webserver, pdf.