ProSMoS

ProSMoS converts 3D protein structures into interaction-matrix models that encode secondary structure element (SSE) types, connection handedness, and spatial interactions to identify 3D structural motifs.

Key Features:

• Interaction Matrix Representation: Converts 3D structures into interaction matrix models encoding SSE types, connection handedness, and spatial coordinates.
• Comprehensive Pattern Analysis: Identifies 3D motifs by analyzing topological architecture and spatial interactions between SSEs while avoiding direct coordinate-based comparisons.
• Beta-Sheet Definitions: Includes detailed beta-sheet definitions for use in structural pattern analysis.
• Database Search Capability: Retrieves database entries matching user-defined structural patterns to detect distant structural similarities.

Scientific Applications:

• Structural Biology: Enables structural biologists to study protein function and evolution through motif-based structural comparisons.

Methodology:

Converts 3D structures into interaction matrices that encode SSE types, connection handedness, and spatial interactions, and performs motif-based searches that avoid direct coordinate-based comparisons, extending beyond topological matches used by TOPS.