Structural Bioinformatics Pharm 201 UCSD Lecture 16

submitted by: Phil
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...

Structural Bioinformatics Pharm 201 UCSD Lecture 15

submitted by: Phil

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.

Structural Bioinformatics Pharm 201 UCSD Lecture 14

submitted by: Phil

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.

Structural Bioinformatics Pharm 201 UCSD Lecture 11

submitted by: Phil

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.

Structural Bioinformatics Pharm 201 UCSD Lecture 10

submitted by: Phil

This is lecture 10 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covers the issues associated with protein structure comparison and delves into the CE method in particular.

Structural Bioinformatics Pharm 201 UCSD Lecture 8

submitted by: Phil

This is lecture 8 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture covered two items. Prof Rik Belew described work he is doing on an HIVortal - a systems biology drill down of HIV. Prof Phil Bourne described the basics of the Gene Ontology.

Structural Bioinformatics Pharm 201 UCSD Lecture 4

submitted by: Phil
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.

Structural Bioinformatics Pharm 201 UCSD Lecture 3

submitted by: Phil

This is lecture 3 from a graduate student class in structural bioinformatics offered at UCSD