The catalytic site atlas (CSA) is a database that displays active sites and catalytic residues of enzymes (ref). The database is regularly maintained, but has not been updated since August of this year. The database currently contains 25,537 entries based on 968 literature references.
The site has a number of search options (located at the top of their page) that include PDB, Swiss-Prot code and EC number.
Below is an example of some of the results that are produced by the CSA. The catalytic residue in this case is an aspartate located at position 93. I would like to see the catalytic residues highlighted differently so that they are can be identified quickly.
The CSA also performs a homology search using Psi-BLAST. This information is very helpful if you are looking for evolutionary relationships between proteins (ref).
The CSA help page is really good (although a number of links to it are dead) if you would like more information or are having trouble interpreting the results.
BenchflyTM has videos of protocols, tips and teachings some of which are quite relevant to macromolecular crystallography. The video quality is excellent. I will look forward to watching their future productions even though the buzz intro gives me the creeps.
We have discussed the controversy regarding the 2009 Nobel Prize in Chemistry that was given for the structure and function of the ribosome. I was also thinking about what a great accomplishment it was and how we could pay tribute.
Here is the idea: Get together 200 of our closest friends of which many of whom would need to wear spandex and short shorts. We would make it a dance tribute and have people attach a balloon to their head for identification. We would then act out the function of the ribosome to music from the 1970s, you know – flute solos and a lot of cow bell.
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Well, I just found out from Molecule of the Day that this idea has already been done, dang – scooped again. Enjoy.
We have a lot of problems that need a structure.
HIV
Cancer
Diabetes
Influenza
Heart Disease
Multiple Scherlosis
Tuberculosis
Alzheimer’s
Arthritis
Autism
Malaria
I have been to the APS Synchrotron quite a few times and realized that there are a couple tricks of where to sleep, if you don’t stay at the Guest House. I often see newbies trying to do the head on the table approach, but in a rolling chair this can be tricky.
So what to do?
1) Sleep on the floor
Pro: plenty of space
Con: the floor is concrete
If you are going to go this route then at least sleep on a coat or put your head on a bag (bring a pillow!).
2) Conference room (located along outer rim of the building)
Pro: decent space, very thin carpet, darker and less noise than being near the beam lines
Con: group members may think you have disappeared, if you don’t let them where you are sleeping
3) Couch
Pro: located near the beam line and a lot better than the floor
Con: bright, few around, maybe on the shorter side if you are tall
I LOVE old school crystallography. I am guessing this is because I have never done it
Images with film. Hand drawing electron density. Structures with wires. Hardcore.
The ultimate list of cryocrystallography and radiation damage, including websites, books, publications and databases. The title and author list of some resources have been shortened for ease of viewing.
Fred points us to an eighteen minute introductory video on structural biology, but unfortunately the English version is not uploaded onto a video hosting site (the French version is here for my friend Julie). I lack the rights to the video so can’t post the English version myself.
I would recommend this video to any relatives that glaze over when you describe your job or perhaps to new graduate students. Enjoy.
The catalytic site atlas (CSA) is a database that displays active sites and catalytic residues of enzymes (ref). The database is regularly maintained, but has not been updated since August of this year. The database currently contains 25,537 entries based on 968 literature references.
group members may think you have disappeared, if you don’t let them where you are sleeping
(couple of chapters)