Tip of the Week: PolyPhen

submitted by: OpenHelix

This week's tip is on PolyPhen, a predictor of nonsynonymous SNP impacts on protein functions. For more information about PolyPhen and SNP functional prediction see the blog post: http://blog.openhelix.eu/?p=6867

SDSC 25th Anniversary

submitted by: Phil

This presentation describes my interactions with the San Diego Supercomputer Center (SDSC) over the past 15 years as part of the celebration of 25 years of SDSC which will take place on October 12, 2010.

Tip of the Week: PSI Structural Genomics Knowledgebase

submitted by: OpenHelix
For more information about this resource see our blog post at URL http://blog.openhelix.eu/?p=4703 on the OpenHelix blog. The PSI Structural Genomics Knowledgebase is a great resource for protein information, including structural information, especially if you are not a structural biologist. In this short movie I will search for a specific Protein Data Bank (PDB) ID & show you the information you can obtain and how it is formatted.

Structural Bioinformatics Pharm 201 UCSD Lecture 18

submitted by: Phil

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.

Structural Bioinformatics Pharm 201 UCSD Lecture 17

submitted by: Phil

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.

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 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 7

submitted by: Phil

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.