protein data bank

This is lecture 18 (the final lecture) from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covers the a brief discussion of some outstanding problems.

This is lecture 17 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covers the features of protein-protein interactions and one method to predict such interactions.

This is lecture 16 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covers molecular graphics and following a brief introduction is a class discussion of the good and bad features of various molecular graphics programs based on an assignment the class had undertaken. Namely: Render a PDB structure of protein kinase A in two or more of the following tools: jmol, Pymol, Chimera (UCSF), ICM Browser (MolSoft) and...

This is lecture 15 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covers a method for studying protein-ligand interactions. Specifically finding off-target binding sites that has implications for studying the side effects and repositioning existing drugs.

This is lecture 14 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covers the principles of assigning protein secondary structure using teh 3D structure as a starting point with a focus on the Kabsch-Sander algorithm as used in DSSP.

This is lecture 11 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covers the field of structural immunology and is presented by Dr. Julia Ponomarenko.

This is lecture 5 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The topic is "Data Representation and the Protein Data Bank" presented by Drs. Peter Rose and Andreas Prlic

This is lecture 4 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The topic is "Know How Best to represent Your Data." Historically the PDB format expresses the Lingua Franca of structural bioinformatics, but it has serious flaws. These will be explored and understood in the context of one replacement - mmCIF. Goal: To understand why good data representation is important.

Fran Berman discusses SDSC's data centric focus and their three key leadership areas.: data-oriented high performance computing, data-storage and preservation, empowering data-oriented communities. Originally posted by SDSC on SDSC's CI Channel at: www.cichannel.org