Archive for May, 2008

A structural biology symposium at Galveston [1]

Tuesday, May 27th, 2008

I went to a structural biology symposium at Galveston. This is a overall high-quality symposium. I’d like to collect whatever I still can remember here.

Keynote speaker is Thomas A. Steitz from Yale Univ. He presented his work on the structural basis of Crick’s central dogma. The key mechanisms in the central dogma are replication, transcription, and translocation. There are a bunch of proteins with experimentally determined structures in each of the 3 key mechanisms.

In replication of eubacterial genomic DNA, there are 4 protein complexes, DNA polymerase III, the beta sliding clamp, the DNAB helicases and DNAG primase. In transcription, there are two important phases, initiation and elongation. With theT7 RNA polymerase crystal structure, Thomas showed how T7 RNA can initiate RNA synthesis and synthesize an 8 to 12 nucleotide transcript. The translocation is accomplished by several states of nucleotide incorporation of T7 RNAP.

It is a very nice presentation and also very cool movie of the central dogma. I can’t help asking, what can computational biologists do to further strength our knowledge of the dogma?

Endless mercy

Monday, May 19th, 2008

The unprecedented earthquake in Sichuan, China makes me very sad. I couldn’t help crying when I saw those heart-torn tragic images of children, women, men, young, seniors.

I wish a steady recover soon!

Scientific game: foldit

Friday, May 9th, 2008

It is actually a surprise to me. A somehow simple idea but very appealing, foldit encourages gamers to involve in designing protein folds. Volunteers/gamers use Fold@home, a software developed at David Baker’s group and also interactively interpret the text and the 3-D images, eventually will help design protein folds.

I haven’t tried it yet, but I’ll keep an eye on it.

Very usful cut command

Thursday, May 1st, 2008

I’m still learning linux (have used it for more than 10 years!).

After download the seqfile from, in order to get all the protein sequence chain names and lengths, just run:

grep ">" pdb_seqres.txt | cut -d" " -f1,2,3 | grep protein | cut -d" " -f1,3 | sed "1,$ s/length://g" | sed "1,$ s/>//g" > seqid_len.txt

seqid_len.txt is what you want!

Awesome, right?!

list empty files

Thursday, May 1st, 2008

There is a combination of commands to get the empty files under current directory:

wc -l * | grep “^\s*0”

Just found it. 🙁