Assemble2

Assemble2 enables interactive construction and semi-automated modeling of complex RNA three-dimensional architectures for structural analysis and design.

Key Features:

• Integration with UCSF Chimera: Integrates with UCSF Chimera to assemble RNA 3D modules from 2D structures and to support visualization and manipulation of models.
• Semi-automated modeling: Supports homology modeling and ab initio methods with optional use of electron density maps for model building.
• Secondary structure editing: Provides interactive editing of RNA secondary structures to refine and optimize modeled conformations.
• Annotated tertiary structure library: Includes a searchable library of annotated RNA tertiary structures for reference during model construction and validation.
• Recurrent task automation: Automates recurrent tasks commonly encountered in structural RNA modeling workflows.

Scientific Applications:

• RNA Structural Biology: Facilitates design and analysis of RNA molecules to identify structural motifs and interactions.
• Drug Design and Development: Supports creation and structural evaluation of RNA-based therapeutics by providing detailed RNA models.
• Educational Purposes: Provides resources and modeling capabilities for teaching RNA structure and modeling concepts.

Methodology:

Implemented in Java and runs on MacOSX, Linux, and Windows; integrates with UCSF Chimera; supports homology modeling, ab initio methods, and optional use of electron density maps.