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 main features of Assemble are:

• prediction of RNA secondary structures
• interactive RNA secondary structure construction and visualization
• semi-automatic generation of RNA 3D models
• connection between the 2D and 3D panels
• torsion angles alteration for any single residue
• translation and rotation of any element from a few atoms to a whole molecule
• easy cut, link of any molecular chains
• ability to manage your own RNA structural library using the MyPDB panel
• ability to search for and save RNA structural motifs to easily fold a 3D region
• embedded refinement tool
• mono and stereo views
• all the computer-intensive tasks are delegated to RNA WebServices
• entirely developed with the Java language. Runs on Windows, Linux and MacOSX
• OpenGL-powered application thanks to the JOGL API project
• open source (MIT) license and free

• 06-09-2010: Assemble 1.0.3 is available as an automatic update. It fixes the automatic update system for Windows. You can find all the details in this blog post
• 06-07-2010: Assemble 1.0.2 is available as an automatic update. You can find all the details in this blog post
• 06-01-2010: availability of a new screencast "How to infer a 3D model from S2S?"
• 05-21-2010: Assemble 1.0.1 is available as an automatic update. You can find all the details in this blog post
• 04-21-2010: Assemble 1.0 is now available. Check the new online documentation to use it efficiently.

• Serialized Thoughts: a blog where you can find news and technical details about Assemble
• S2S (Sequence to Structure): a project complementary to Assemble
• RNA Web Services: lists all the RNA Web Services consumed by S2S and Assemble
• 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 middle-layer between the graphical tools and the RNA Web Services
• 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).