pdb

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 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.

This is lecture 7 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ The lecture illustrates to students how biocurators accept and process data both within the Protein Data Bank (PDB) and UniProt with the goal of helping students understand the strengths and weaknesses of the data they analyze.

This is lecture 6 from a graduate student class in structural bioinformatics offered at UCSD see http://www.sdsc.edu/pb/edu/pharm201/ Teh title is "the multipolar parametrization: an alternative representation of protein shape/structure" presented by Dr. Apostol Gramada

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.

Dr. Helen M. Berman, Director of the Protein Database (PDB), Rutgers University. Dr. Berman is internationally renowned for her development of protein and nucleic acid databases. Her research interest is in the application of Bioinformatics to protein structure.