LEMod6vsELMod4

Submitted by Patrick L. Williamson on Tuesday, 11/2/2010, at 4:00 PM
Overlapping Structures

Pauling articles

Submitted by Patrick L. Williamson on Monday, 10/4/2010, at 8:25 PM

Pauling's article on protein helices can be found here, and his article on sheets can be found here.

Databases of Protein Structures

Submitted by Patrick L. Williamson on Sunday, 9/12/2010, at 10:33 PM

Most well-determined structures (protein or nucleic acid) are publicly available in more than one database.  The two most prominent are:

The primary depository for protein structures, the Protein Data Base, has a site which can be found here

The National Center for Biotechnology Information (NCBI) maintains a protein structure database, derived from the PDB, but with the structure information in a different file type.  The front door to this data base can be found here.

Not all protein structures have actually been determined - modeling protein structures based on sequence data is an active business.  The Swiss-Prot database of modeled structures was the first to make such models available here.

Somewhat later, the University of California at San Francisco set up a separate model database, which is found here.

 

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CMCC Web site

Submitted by Patrick L. Williamson on Saturday, 9/4/2010, at 1:35 AM

The web site associated with our text Crystallography Made Crystal Clear is found here.

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Links to Protein Visualization Software

Submitted by Patrick L. Williamson on Saturday, 9/4/2010, at 1:35 AM

The old workhorse for this course is Protein Explorer, and you can get to it through here

 

The NCBI structure viewer is called Cn3D, and can be obtained here.   The program does not operate from this site - you download it to your own platform, and it is then called up locally when needed. 

 

Rhodes likes the structure viewer from the Swiss-PDB site, known as DeepView, which can be obtained here.  This program allows you to change the amino acid at particular positions in a protein, and then look to see what  consequences (might) ensue.

The wave of the future is probably the Chimera software, available here.  This is definitely not compact or efficient software (it operates at a crawl on my old laptop), but it is very powerful, with a variety of add=on capabilities (such as docking software), and very nice ray-traced images.

 

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Reserve Reading List.2Sept

Submitted by Patrick L. Williamson on Saturday, 9/4/2010, at 1:42 AM
The PDF file below lists books currently on reserve in the Science Library. It includes copies of the textbooks from the course. In addition, there are other books on the subject, including some that I've used or considered using as textbooks instead of the ones currently on the list. Finally, there are some books on the list that contain illustrations of the relationship between objects in normal space and their Fourier transforms.

Amino AcidTable

Submitted by Patrick L. Williamson on Saturday, 9/4/2010, at 1:41 AM
The table that forms the basis for the first exam.

Project Proteins

Submitted by Patrick L. Williamson on Saturday, 9/4/2010, at 1:46 AM
The requirements for completion of the student presentation section of the course are given in the PDF document below, as is a list of the proteins from which the project must be chosen. Each student must do a different protein, and choices from the list will be allocated on a first come, first serve basis, where the choice can be made only by an email to me, confirmed by a return email from me. All choices must be finalized by Friday, Oct 8. This and other deadlines are given in the document.
 

Taking Notes