IMAAAGINE

IMAAAGINE searches the Protein Data Bank (PDB) for hypothetical three-dimensional amino acid side-chain patterns to identify potential structural motifs in proteins.

Key Features:

• Flexible Query Design: Allows definition of a sequence of 3 to 8 amino acids with minimal side-chain descriptions and specification of generic types such as acidic, basic, or hydroxyl-containing residues.
• Partial Distance Specification: Permits specification of only a subset of inter–side-chain distances in the query.
• Pattern Conversion and Search: Converts user-defined amino acid sequences into geometric search patterns used to interrogate PDB structures.
• Pattern Matching to PDB: Searches PDB structures to identify conformations that match the specified geometric pattern, including motifs not previously cataloged.
• Demonstrated Motif Types: Applied to configurations such as arginine stacks, serine–acid group arrangements, and multiple catalytic triad–like structures.

Scientific Applications:

• Novel Motif Discovery: Exploration of hypothetical 3D side-chain arrangements that may influence protein function or interactions.
• Protein Engineering: Identification of candidate side-chain configurations for design or modification in protein engineering.
• Drug Design: Support for studies identifying unconventional side-chain arrangements relevant to ligand binding or target sites.
• Enzyme Mechanism Studies: Analysis of catalytic triad–like and other arrangements relevant to enzyme mechanisms.

Methodology:

Converts user-defined amino acid sequences into search patterns and interrogates PDB structures to identify conformations matching the specified pattern, including novel or uncharacterized motifs.