MOE's LigPlot gizMOE rules!!!

I just tried to use MOE (Molecular Operating Environment) to draw a ligand/protein interaction diagram. I fell in love with these kind of graphs the first time I saw them, from the original LigPlot software. I love the way they represent the fundamental interactions without the fuss of 3D structures. I did once suggested the use of them rather than confusing 3D structs as output of a distributed docking program at my previous university. Look at the picture above, and it shows how a given ligand interacts with neighboring residues by means of hydrophobic contacts (the small sun-like drawings) or hydrogen bonds (the green line with distances)

Anyway, right now I just needed a couple of shots showing how the lipocalins' binding pockets are devoid of h-bond anchor points, if compared to other classes. Unfortunately, LigPlot for windows does not come without the hassle of having to mail his author, so I had to wait until I got back to work. Where we have MOE and their own implementation of the cake.

This morning, then, I loaded up three Lipocalins structures, plus one Exopeptidase, one Protease, and one Oxido-Reductase for comparison and hey!, presto, I have six wonderful shots lending weight to my assertion.


(picture here isnone of them, just a snapshot from MOE's website - again, green lines show h-bonds (without distance, but they have directionality as added bonus) - the green balls are apolar residues in hydrophobic contact.) I am not sure what the blue line is. Oh, there it is: When the hydrogen bond is formed with the residue sidechain, the arrow is drawn in green. Hydrogen bonds to the residue backbone are drawn in blue, with an additional dot drawn at the residue attachment point.
I just wish my current work was more structure-based to be able to play some more with all these cool softwares. Well, may be my next job? or life? who knows?

Do Penguins topple when Planes fly over?

I found this while looking for a penguin gif:

On November 2nd timothy of Slashdot asked if penguins topple when planes fly over? The British Antarctic Survey has organized a the first expedition to explore this theory and came back with news now.

The short answer: No, penguins don't fall over.

In November the BBC released a story covering a research project that took UK scientists to the South Atlantic. They wanted to discover if there is any truth in the tale that many aircraft pilots told the public.

Pilots often reported that when they were flying over a colony of penguins the birds were watching the planes, but instead of moving their bodies to follow the aircrafts they only moved their heads which lead them fall backwards over. This was said to happen to the entire colony of penguins and not just to some individuals.

If this was true, it could lead to a serious problem. Penguins only live in colonies around the antarctic and there aren't that many. If the aircrafts disturb their breeding pattern future of penguins is uncertain. The research project was acknowledged by fears that breeding patterns of the birds may be disturbed and interupted by aircraft activity such as jets and helicopters from aircraft carriers.

From the beginning of this research project there was no evidence that penguins actually fall over. All the scientists knew about were myths of aircraft pilots who supposedly watched entire colonies topple.

The researchers from the British Antarctic Survey went to South Georgia, an island belonging to the Falklands, in order to observe a colony of King Penguins. With help of the Navy and their ice patrol vessel HMS Endurance the scientists let helicopters fly over the colony of penguins and watched the birds.

The results were different from what pilots formerly reported. The birds did not fall backwards over or watched the helicopters. Instead the penguins went quiet and some moved away from the disturbing noise. Though, after the helicopters were gone the penguins moved back to their regular places. Please read the entire report.

Frankly, I can't believe they really went to check!!! LOL

more info here.