Assemble2 has been used to model the interaction between the T-box leader ProI Stem I of B. subtilis and a tRNA. The 3D model makes the cover of the issue of Nucleic Acids Research.
Assemble2 uses RNA algorithms and RNA data to automate several steps (2D structure prediction, 3D refinement,…). The default behavior of Assemble2 is to use the algorithms and data made available through dedicated Web services hosted at http://arn-ibmc.in2p3.fr/api/.
To speed up Assemble2, you can host these Web services on your own machine (or any machine in your local network). Initially, the installation process was a little bit cumbersome. That’s why i have provided recently a CentOS Virtual Machine to deploy your own Web services more easily.
But now this process has been simplified. You need to install and configure two main components:
- PyRNA: a Python library providing scripts to download the RNA algorithms and the RNA data needed for Assemble2. PyRNA provides also a script to launch the Web server hosting the Web services consumed by Assemble2.
- MongoDB: a NoSQL database used to store the data needed for Assemble2.
The following sketch gives you an insight into the relations between all these components.
All the installation steps are fully described in an updated version of the documentation (in “1.4. Local installation of the RNA Web Services (optional step)”). Don’t hesitate to contact me for details or for any remark or comment.
“Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and maintenance. The few available structures of the eukaryotic ribosome reveal that it is more complex than its prokaryotic counterpart, owing mainly to the presence of eukaryote-specific ribosomal proteins and additional ribosomal RNA insertions, called expansion segments. The structures also differ among species, partly in the size and arrangement of these expansion segments. Such differences are extreme in kinetoplastids, unicellular eukaryotic parasites often infectious to humans. Here we present a high-resolution cryo-electron microscopy structure of the ribosome of Trypanosoma brucei, the parasite that is transmitted by the tsetse fly and that causes African sleeping sickness. The atomic model reveals the unique features of this ribosome, characterized mainly by the presence of unusually large expansion segments and ribosomal-protein extensions leading to the formation of four additional inter-subunit bridges. We also find additional rRNA insertions, including one large rRNA domain that is not found in other eukaryotes. Furthermore, the structure reveals the five cleavage sites of the kinetoplastid large ribosomal subunit (LSU) rRNA chain, which is known to be cleaved uniquely into six pieces, and suggests that the cleavage is important for the maintenance of the T. brucei ribosome in the observed structure. We discuss several possible implications of the large rRNA expansion segments for the translation-regulation process. The structure could serve as a basis for future experiments aimed at understanding the functional importance of these kinetoplastid-specific ribosomal features in protein-translation regulation, an essential step towards finding effective and safe kinetoplastid-specific drugs.”
This is not anymore supported. You should rather have a look at this post…
By default, Assemble2 delegates the work for several tasks (2D prediction, 3D motifs search and threading,…) to web services hosted on my own server. If you want to speed up Assemble2, you can deploy your own web services. I have created a Virtual Machine (VM) with VirtualBox and CentOS 5.9 (32-bit) to allow you to do that more easily. It can be deployed on the same computer than the one used to run Assemble2 or on different one in your local network. Follow these steps:
- download and install VirtualBox and its Extension Pack
- download the CentOS VM and load it into VirtualBox (please be patient, it is 1.81Go)
- before to start the CentOS VM, configure its Network to use the Bridge Adapter and to set the Promiscuous Mode to “Allow VMs”
- start the CentOS VM and log in as assemble2 (passwd: assemble2)
- open a terminal. In a tab, check the IP address of your VM by typing ifconfig
- In a second tab, go into the rna-js directory (cd rna-js) and launch the webserver hosting the webservices: ./lib/server.js -conf ./lib/assemble2-config
- launch Assemble2 from your host OS (MacOSX, Linux, Windows), and set the location of the web services (in this example, it should be http://192.168.1.24:8000/api)
If you want to change the port used by the server (8000), open the configuration file assemble2-config, edit the line “config.webserver.port = 8000;” and restart the server.