Assemble proposes an intuitive graphical interface to study and construct complex three-dimensional RNA structures. When an RNA tertiary structure is opened with Assemble, it is automatically annotated with a secondary structure definition. This secondary structure can be used as a map to analyze the original tertiary structure. Using a secondary structure definition, Assemble can also produce a first draft of a 3D Model. Then the construction process can be pursued "by hand" using several widgets.

The Assemble's main features are:

• semi-automatic generation of a 3D structure from a user-defined RNA secondary structure
• easy RNA secondary structure construction and visualization
• torsion angles alteration for any single residue
• translation and rotation of any element from a few atoms to a whole molecule
• easy cut, link and stacking of any molecular chains
• embedded RNA tertiary motif repository to easily fold a 3D region according to an RNA tertiary motif already observed at high resolution
• embedded refinement tool
• depth-cueing, mono and stereo views
• entirely developed with the Java language. Runnable under Windows and UNIX systems
• OpenGL-powered application thanks to the JOGL API Project
• open source (MIT) license

• 06-15-2009: Assemble is now available to anyone. Check the Downloads page.
• 04-30-2009: the "official" beta-testers have received the instructions to download the Release Candidate 1 of Assemble 1.0
• 04-14-2009: you can find news and technical details about Assemble on the "Serialized Thoughts" blog
• 03-27-2009: the release of Assemble 1.0 is planned for the second half of April 2009
• 02-08-2009: the new website is online and under construction. No official release of the new Assemble until few weeks. If you want to be an official beta tester, send us an email

• Assemble is a construction tool. At now, it has not been implemented to produce high quality pictures of the 3D model. Consequently, its rendering abilities are limited to what is needed for the construction process. If you need to produce such pictures, export your model as a PDB file and open it with tools like PyMOL, Chimera or VMD

• Serialized Thoughts: a blog where you can find news and technical details about Assemble
• S2S (Sequence to Structure): a project complementary to Assemble
• PARADISE: S2S and Assemble are constructed over the PARADISE engine. This engine sums up the technologies necessary to construct more easily our tools:
  • the RNA concepts displayed and manipulated (helices, single-strands, tertiary and secondary structures, structural alignments,...)
  • the construction and deployment of a calculation layer embedding RNA algorithms
• The non-Watson-Crick base pairs and their associated isostericity matrices: this publication describes the base-pair symbols used in the 2D scene
• RNAView: generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions.
• Vienna RNA Package: several stand-alone programs for the prediction and comparison of RNA secondary structures.
• The JOGL API Project: the Java binding for the OpenGL API used by Assemble
• The Java Agent DEvelopment Framework: used to develop the calculation layer hosting the RNA algorithms
• MyDoggy: the Java docking framework to make the graphical interface of Assemble more attractive
• Tango Desktop Project and FamFamFam: the icon sets used for Assemble

The Assemble project is managed by Dr. Fabrice Jossinet. It is developed in the laboratory of Pr. Eric Westhof at the "Institut de Biologie Moleculaire et Cellulaire" of Strasbourg, France (Team "Architecture et Réactivité de l'ARN", UPR 9002 of CNRS, Université de Strasbourg).