3Motif

3Motif visualizes protein sequence motifs within three-dimensional protein structures by mapping motif patterns onto structures from the Protein Data Bank (PDB).

Key Features:

• 3D Motif Mapping: Maps discrete sequence motifs such as PROSITE patterns and eMOTIFs onto three-dimensional protein structures.
• Flexible Motif Querying: Accepts queries including protein sequences, keywords, structural information, or motif definitions and supports regular expression-like motif searches.
• Position-Specific Matrix Support: Converts multiple sequence alignment blocks into eMATRIX position-specific scoring matrices for motif visualization.
• Motif Property Visualization: Displays motif attributes including sequence conservation strength and solvent-accessible surface area using color-shaded structural representations.
• Chime-Based Structural Manipulation: Enables interactive exploration and manipulation of three-dimensional protein structures using the Chime plugin.

Scientific Applications:

• Protein Family Classification: Identifies conserved sequence motifs to group proteins into families based on shared structural and functional features.
• Protein Functional Annotation: Examines spatial positions of conserved motifs to infer functional roles of residues in protein structures.
• Evolutionary Protein Analysis: Studies conservation and structural placement of sequence motifs to investigate evolutionary relationships among proteins.

Methodology:

3Motif searches the Protein Data Bank (PDB) for matches to user-defined sequence motifs, maps identified motifs onto corresponding protein structures, and calculates motif properties including sequence conservation strength and solvent-accessible surface area for visualization.