Amino Acid Table

Submitted by Patrick L. Williamson on Thursday, 9/3/2009, at 12:28 PM

The table in the PDF file below is the subject of the first exam. 


Student Presentations

Submitted by Patrick L. Williamson on Thursday, 9/3/2009, at 11:58 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 9.  Additional deadlines are given in the document.


Library reserves

Submitted by Patrick L. Williamson on Thursday, 9/3/2009, at 12:30 PM

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.

The list is here:


CMCC Web site

Submitted by Patrick L. Williamson on Monday, 9/21/2009, at 9:07 PM

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


Databases of Protein Structures

Submitted by Patrick L. Williamson on Thursday, 9/3/2009, at 1:23 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.



Links to Protein Visualization Software

Submitted by Patrick L. Williamson on Thursday, 9/3/2009, at 10:46 PM

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.



Structural Biology meeting

Submitted by Patrick L. Williamson on Tuesday, 9/15/2009, at 9:50 AM

Got the following letter....


Dear Colleagues:

On behalf of University of Connecticut Partnership for Excellence in Structural Biology we are pleased to invite you to the 6th annual North Eastern Structure Symposium (NESS).

This year, NESS will be held on Saturday, October 3rd at the University of Connecticut Health Center in Farmington, CT.  The featured topic is "Structural Biology of Host-Virus Interactions". Please visit our web site ( for the list of speakers, agenda, directions and online registration.

The deadline for discounted early registration is this Friday, September 18th. The registration fee includes admission to the scientific sessions, refreshments, and lunch. There will also be a poster session and we strongly encourage students & post-docs to participate. There will be a $100 cash prize for the best poster. The maximum dimensions for a poster is 4'x 6'.

NESS is sponsored by the Partnership for Excellence in Structural Biology at the University of Connecticut.  The partnership was established in 2005 to form an interactive research and training environment in structural biology across multiple departments, schools and campuses at the University. NESS has grown into a significant regional meeting. We encourage you to attend this exciting and thought-provoking symposium.