Dart web server tool

Well, we created a new HeadingElement , using the h3 named constructor feature of Dart and saved a reference in heading. Next, we changes the text of the heading element and finally, we inserted it as the first child of the div with the class of dogs. Names should start with a capital letter, and the list looks sort of out of place. Using Dart, we can get a reference to the list and go through the names, fixing the case issue for each item.

Make sure it gets called in the main function. Save your changes and refresh your browser. You should see something like this:. The title we added previously, is the 0th, or first child of the element.

Once we have the reference, we create a map, which allows us to fix each element in place, using the Dart string interpolation syntax. Since the reference we obtained is directly linked to the DOM, the values of the list are changed immediately, without further intervention required.

Update the page title in the main function to say something more appropriate. You can put in anything you want, I changed mine to:. Create a new function called alignFooter with the following content:. Make sure it gets called in main , then save and refresh your browser. The footer should now be properly aligned:. This time, we used the querySelectorAll , a very handy function that will select ALL the elements that fit the criteria. In our case, we have to use the first keyword to give us the first element in the list, because we know that we have only one footer on the page.

Did you notice that official is spelled wrong in the footer? How can we find and fix it? The spelling is fixed! But… Our link has disappeared? Powerful and configurable, a built-in OAuth 2. An expressive test syntax with full integration allows for functional tests that don't rely on mocks. Full access to the framework allows testing database updates and more. Conduit is relied upon to power advanced applications in production for several companies, including TaxiTecnic.

Conduit is supported by over automated tests, guaranteeing the stability of each release. The computational engine beyond the server makes use of the 3DNA software suite together with a collection of home-written python scripts. DNA often changes its conformation as a result of interactions with various ligands; especially binding to proteins can result in large conformational changes such as helical kinks 1 or local helical untwisting 2.

These play an important roll in providing complementarity to the protein binding surface and contributing to the interaction specificity 3. In order to fully understand the nature of the conformational changes taking place upon complex formation, 3D, atomic-resolution structures are required.

Experimental methods such as X-ray crystallography and nuclear magnetic resonance spectroscopy NMR but also computational approaches such as macro-molecular docking are important techniques for obtaining such 3D structures or models. Most techniques make use of 3D-structural models of DNA at some point along the structure calculation pipeline. NMR for instance can benefit from the regularity in the structure of double-stranded DNA by using a model as starting point for structure calculations, thereby compensating for the lack of long range structural information.

For macro-molecular docking, a starting model is often required as experimental structures might not be available. Often, starting from multiple models with different conformations improves the results. Finally, as last example, homology-modeling programs require a template model as starting point for the homology building process.

The regularity in the structure of double-stranded DNA makes it especially suitable for modeling. Various software packages are available that convert a user specified base-pair sequence into a 3D structure using regular nucleotide building blocks 4—8.

However, most of these software packages, some of which are available via web-servers 4 , 7 , are only able to generate models in ideal canonical conformations 5 , 7 or in conformations mimicking that of a free unbound structure 4. The structures of double-stranded DNA in complex with various ligands often show considerable conformational changes compared to their unbound counterparts 9— Only a few existing programs, such as NAMOT 8 and NAB 6 , offer options to introduce custom bends in the generated DNA conformation and give control over all local parameters; they however require some expertise from the user and are not available as web servers.

The generation of models is accomplished by modification of the well-established rotational and translational parameters that describe the position of one base to its Watson—Crick counterpart and of two successive base pairs relative to one another It has been demonstrated in the past that rebuilding a double-stranded DNA structure using these parameters results in a near native structure 5.

The only exceptions are local changes in the sugar and phosphate backbone conformation. The 3DNA software 5 is used to generate a 3D-structural model from the modified parameters.

The server accepts a nucleotide sequence, a base pair step parameter file or a DNA-containing PDB coordinate file as input. The server returns 3D-structural models with the desired conformation as well as a collection of analysis and intermediate files. Several additional and convenient functions are available to control the markup of the resulting PDB coordinate files, for instance to prepare them for use in the macro-molecular docking program HADDOCK 14 , 15 also developed in our group.

For the same purpose the server can automatically generate a DNA restraint file 16 as an additional feature. Local bending is often at the origin of double-stranded DNA distortions when in complex with various proteins 9— This type of bending can be described in terms of the vector between two successive base pairs a base pair step.

The length of this vector Figure 1 , thick black arrows describes the distance between the two base pairs in a base-pair step, also known as Rise. It usually does not vary much. In unbent canonical DNA, these vectors align with the Z -axis that represents the main helical path of the structure Figure 1 A.

When the DNA is bent, then the position of the vector relative to the global reference frame describes the magnitude and orientation of the bend angle. The magnitude of the bend corresponds to the vector component projected on the Y — Z plane and its orientation to the component projected on the Y — X plane Figure 1 B.

The accumulation of successive vectors then determines the overall bend in the structure. Vector projections are normalized for illustrative purposes. In addition, 2 full sample projects are included. Available Platforms. Debug Server for debugging and protocol testing. Full MS Help 1.