MaDCaT

MaDCaT maps inter-residue distances to identify and categorize tertiary structural motifs in proteins, enabling structural similarity searches and assessment of motif designability.

Key Features:

• Mapping Distances for Topology: Maps inter-residue distances to categorize protein topology and define tertiary motif geometry.
• Structural Similarity Search Methodology: Prioritizes detailed geometric matches over global topological agreement to detect specific tertiary structural motifs.
• Designability Assessment: Evaluates designability of hypothetical tertiary motifs by analyzing their utilization rates in natural proteins and determining how readily they can be realized with natural amino acids.

Scientific Applications:

• Protein Design and Structure Prediction: Provides insights into sequence constraints required to encode designable tertiary structural motifs, informing de novo protein design and structure prediction.
• Structure/Sequence Link Establishment: Identifies sequence preferences required to stabilize specific tertiary motifs, facilitating establishment of links between protein structure and sequence.

Methodology:

Uses a structural similarity search that focuses on detailed geometric matches rather than broad topological similarities, maps inter-residue distances to categorize topology, and assesses designability by analyzing motif utilization rates in natural proteins.