skip to main |
skip to sidebar
I would like to submit two confidential files to the protein Morph Server which contain heteroatoms – the cofactors FAD and NADP+. The server notified me to contact the site maintainers directly for this service. I’d like to calculate 20 frames between the structures.We have the option of a private site on the submission page (http://molmovdb.org/cgi-bin/submit.cgi). In that case the created web-page won't be added to any databases and won't be searchable. The only person that knows the created link will be able to see it. In case these people won't get email with results they should try manually to open the page http://molmovdb.org/cgi-bin/morph.cgi?ID=given_id where given_id is the ID given at the submission. For example http://molmovdb.org/cgi-bin/morph.cgi?ID=585109-19896
We have a new integrin ectodomain structure with two molecules in the asymmetric unit. There is a small amount of breathing at what we call the headpiece-tailpiece interface when the two molecules are compared. This is very important to some molecular dynamic simulations that we are doing. The movement between the two molecules is small, a few degrees, but involves large units of the molecule. We would like to use the morph server to extrapolate, rather than interpolate, this motion. I have looked at your description of frodo lite and this seems a good approach. So, following up our meeting at Yale, we would appreciate some help with this.
By "extrapolate" I believe you mean that you want to predict an unknown conformation from one or two known ones. FRODA can in fact be run in "undirected" mode and this will sample the accessible phase space consistent with sterics and the hydrogen bonding pattern. However it does not pick out the desired conformer from the large number of generated conformers. Certain assumptions are also made about the hydrogen bonding pattern which may result in the desired conformation not being present at all in the generated ensemble.
Instead of FRODA, perhaps you want to try our soon to be announced motion prediction tool, the Conformation Explorer. It is specifically designed to predict the motion of domains. Domains are often too large and slow moving to be dynamically characterized by MD. Further complicating matters, the motions are stochastic and the MD force fields are far from perfect; therefore the motion may not be observed even when the trajectory has been computed for a period of time experimentally
known to be sufficient. We have been successful in predicting large scale domain hinge bending motions for five proteins, including biotin carboxylase, glutamine binding protein, and MurA.
We do need to know something about the conformation which is to be predicted, however, in order to pick the right conformer out of the ensemble. If it binds a small ligand, for instance, we can find the holo structure given the apo by computing stability, free energy of ligand binding, gyration radius, and other quantities. Your use of the word "extrapolate" suggests you may have some geometric information about the target conformer which we can use.
I have found your Morph Server and CNS script very useful, particularly for providing a good visual aid for presentations and such. I am currently preparing some manuscripts for several protein crystal structures, which have two different conformational states. I was considering using your script to generate a morph of the two states, and creating an animated video of the conformational change to be included in the supplementary material of the paper. I was wondering if you had any requirements or wishes regarding the citation of your script. Obviously we would cite your work in the paper itself, but I was wondering if you had any other preferences for the inclusion of a citation in the supplementary material, such as putting a citation at the end of the animation. Any recommendation you could provide would be much appreciated.Best to just citehttp://papers.gersteinlab.org/papers/molmovdb-update-nar/http://papers.gersteinlab.org/papers/morphs-nar/in the paper and end of suppl. material (if possible).
Is the morph server functioning correctly? I’ve used it for several years for course projects but students are having difficulty with it this year. We have a new network system and I am trying to find out if it is on your end or ours where the problem lies.The morph server has experienced an unexpected surge in popularity recently. We are discussing upgrading hardware and this should help. Also we will be investigating whether we have software issues that need to be addressed. I can tell you that new submissions are successfully being added daily, so the server does work. My suggestion for fast results is to try small proteins and ask for a small number of frames (maybe just 4 or so). Also we have three different morph engines as you may appreciate, so if one doesn't work you might try another the next day. Please don't flood our server with multiple submissions of similar proteins in a single day though.
I have a morph I created some time ago that illustrates an essential motion in the protein I study. I'd like to have the morph as part of my thesis talk. Can I turn it into a movie that I can store on my computer and have as a part of my power point presentation (in other words, can I have a copy of it so that I don't have to access the webpage?). How do I do this? Are there obvious directions on teh webpage that I"m just missing? On the jmol morph page you will see a link that says: Orient the molecule to your liking and then: Generate high-res gif Unfortunately it is just a wireframe animation. I had it set to do cartoons but for some reason it's back to wireframe now. Alternatively, you can download the interpolated trajectory, then animate using vmd or jmol. Look for an NMR-formatted PDB file called movie.pdb here: http://www.molmovdb.org/uploads/b061676-11139
