R3DMCS

R3DMCS visualizes structural variation in RNA motifs across experimental 3D structures, enabling comparison of RNA nucleotides and investigation of conformational changes or conservation across species.

Key Features:

• Cross-structure motif comparison: Compares selected RNA nucleotides across all 3D structures of a given molecule from a given species.
• Rfam family mapping: Compares RNA motifs across all 3D structures mapped to a single Rfam family.
• Automated retrieval and alignment: Retrieves, aligns, annotates, organizes, and displays 3D coordinates of corresponding sets of nucleotides from other 3D structures starting from one instance of the motif.
• Functional state exploration: Enables exploration of conformational changes of motifs due to 3D structures being solved in different functional states or different experimental conditions.
• Cross-species conservation analysis: Supports investigation of conservation of 3D structure across species.
• Sequence-structure relationship analysis: Enables analysis of changes in 3D structure due to changes in sequence.

Scientific Applications:

• RNA structural biology: Compare and visualize RNA motifs across multiple 3D structures to study structural variation.
• Comparative RNA analysis: Investigate conservation of RNA 3D structure across different species.
• Functional state analysis: Explore conformational changes in RNA motifs associated with different functional states or experimental conditions.
• Sequence-structure studies: Analyze how changes in RNA sequence affect 3D structure.

Methodology:

R3DMCS retrieves, aligns, annotates, organizes, and displays 3D coordinates of corresponding sets of nucleotides from other 3D structures starting from one instance of the motif.