seeMotif

seeMotif visualizes sequence motifs on protein structures from the Protein Data Bank to enable exploration and characterization of motif spatial context.

Key Features:

• Interactive visualization: Visualizes sequence motifs directly on 3D protein structures and enables examination of spatial arrangement and conformation of multiple motifs across related structures.
• Integration with PDB structures: Leverages the Protein Data Bank repository and accounts for differences between PDB sequences and sequence-database entries such as shorter lengths or missing residues.
• Complementary mapping strategies: Employs two complementary strategies for selecting appropriate structures and accurately mapping motifs onto protein chains to handle sequence variations and gaps.
• Support for large-scale genomic studies: Combines sequence and structural data to aid interpretation of protein function as more structures from previously uncharacterized families become available.

Scientific Applications:

• Motif discovery and annotation: Facilitates annotation of proteins with functional signatures by mapping discovered sequence motifs onto experimental structures.
• Functional role characterization: Aids characterization of motif function by placing motifs in their structural and spatial context within proteins.
• Synergistic relationship analysis: Enables analysis of spatial relationships and potential interactions between different motifs on protein surfaces.

Methodology:

Selects structures from the Protein Data Bank and maps sequence motifs onto protein chains using two complementary strategies to accommodate sequence discrepancies and gaps between PDB entries and sequence databases.