AlphaLasso

AlphaLasso identifies and analyzes lasso-type topologies in protein structures, including AI-predicted models, to enable large-scale structural motif discovery.

Key Features:

• Lasso motif detection: Identifies lasso motifs closed by cysteine, amide, ester, thioester, or user-specified bridges.
• Structure smoothing: Smoothes protein structures to facilitate lasso motif analysis.
• Topology mapping: Creates topology maps for visualizing lasso structures.
• Similarity search: Searches for proteins with similar lasso motifs.
• Model evaluation: Performs in-depth evaluation of structural models.
• Metadata annotation: Annotates lasso motifs with relevant metadata.
• Precomputed database: Provides precomputed lasso topologies for high-quality AlphaFold Database models, including over 14 million proteins with cysteine-closed lasso motifs and 2.2 million complex lassos.
• User structure comparison: Supports comparison of precomputed lasso classifications with user-submitted structures.

Scientific Applications:

• Drug design: Enables discovery of novel therapeutic targets through analysis of complex lasso motifs in proteins.
• Biopolymer industry: Supports development of biopolymer applications via structural motif characterization.
• Large-scale structural biology: Facilitates broad-scale analysis of AI-predicted protein structures from the AlphaFold Database.
• Cross-disciplinary research: Supports studies in biology, biophysics, chemistry, and mathematics through mathematically defined topology analysis.

Methodology:

AlphaLasso applies mathematically defined topologies to protein structures for automated identification of lasso-type motifs, building on the foundation of lasso peptides to detect complex lasso motifs as macroscopic analogs in proteins.