Tag Archives: protein structure

Ubiquity – coding something useful in less than 20 minutes

Ubiquity is the new experimental extension to Firefox that will (I’m sure it will) make enormous impact on the way we use the browser. It allows to remix various services and extend functionality of the browser in very easy way (if you don’t get the point of Ubiquity yet, I recommend watching the video that came with official announcement; I needed to see that – description didn’t tell me much about how powerful it can be).

I didn’t have much time to play with it yet, but in spare 20 minutes I attempted to code a command that would show me the image of a structure from PDB given its code and eventually take me to its homepage. Suprisingly it was very easy (and I’m not a JS coder). The source is pasted below.

  name: "pdb",
  description: "Goes to Protein Data Bank given PDB code.",
  icon: "",
  help: "You can specify the PDB code and pressing enter will take you to particular structure's homepage." +
    " If you type pdb code and press arrow down, you should see an image from PDB site.",

  takes: {"PDB code": noun_arb_text},

  execute: function( directObj) {
    var pdbcode = directObj.text;

  preview: function( pblock, directObj ) {
    var pdbcode = directObj.text;

    pblock.innerHTML = "Preview of the structure:<br/>";
    pblock.innerHTML += "<img src=\"" + pdbcode + "_bio_r_250.jpg\" />";


It of course could be improved by using also a selected text, or allowing to keyword search the PDB (or basically any other biological database), but its current functionality suits me just fine. Ubiquity is not yet such a stable platform as Greasemonkey (or Chickenfoot), but it’s worth to keep an eye on it. I’m sure we will read sooner or later an article in peer-reviewed journal describing Ubiquity commands for life sciences :).

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Posted by on August 27, 2008 in Software


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BadA head structure

Modularity is one of the most interesting features of the trimeric autotransporter adhesins, and probably one of the most frustrating. As I wrote before, domain annotation is quite difficult, especially that these proteins can have often few thousands residues in length.

BadA, the major adhesin of Bartonella henselae, is probably the best known large TAA out there. Its sequence served us as a unofficial benchmark for domain annotation tool. Its head consist of three domains, one resembling head of YadA and two others which we claimed are similar to Hia head domains. The claim at the moment of starting this project wasn’t supported very well – Evalues of HHpred alignments were around 1 (of course all less sensitive tools didn’t see anything), but we knew they must be similar (because that two,three conserved residues were at exactly where we expected). Crystal structure of these two domains from BadA couldn’t be solved directly, so we’ve attempted molecular replacement and that worked. On the picture above you can see three known head structures for TAAs, BadA (ours), Hia and YadA (full BadA head model in on the right) and arrangement of corresponding domains in all three proteins. The whole story and lots of pretty pictures (you must see EM figures) was published today yesterday in PLoS Pathogens (OA).

Today the story isn’t so exciting as it was at the beginning. Currently HHpred easily finds domains from Hia and BadA similar with high probability – it’s an advantage of bigger database size and more mediating sequences. But I’m still pretty happy about how it went – such projects build confidence in one’s analysis skills.

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Posted by on August 9, 2008 in bioinformatics


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Breaking news: structure of usher pore solved

My colleague is at Grenoble on the conference about host-pathogen interactions. Today he sent me important news: Gabriel Waksman (that’s not surprising to anybody interested in structural biology of bacterial pathogenesis) showed structure of usher pore – soon to be published.

Why is that important? Usher is a membrane part of two component system responsible for assembly and transport of fimbriae/pili in gram-negative bacteria – pretty essential element in these organisms. This protein was identified in early 90s (or even earlier) and for quite a while lots of people tried to solve/predict/model its structure. Its structure was assumed to resemble porin – but a large insert right in the middle of beta-barrel gave lots of problems in predicting correct topology. Now we know (at least my colleague saw it, we need to wait) how the final structure looks like and I was also told that its functional aspects have a big relevance to other secretion systems. Have a look on this protein when it’s out (I’ll post definitely about it) – I think you will be surprised even if nuances of host-pathogen interactions are not very appealing to you.

Studying any niche area on the molecular level can be very rewarding. Novel protein fold by itself is not a big deal anymore (it used to be – browse through archives of Nat. Struc. Biol. from several years ago). But putting this novel structure in well known functional context and understanding constrains that led to a new solution is still considered a first-class science.


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