SuperLooper

SuperLooper models and places protein loops in globular and membrane proteins to support structural analysis of loop conformations.

Key Features:

• LIP database: repository of approximately 500 million segments from water-soluble proteins with segment lengths up to 35 residues enabling sequence-based screening for candidate loops.
• LIMP database: collection of 180,000 membrane loop sequences tailored for membrane protein loop modeling.
• Scoring system: evaluates loop candidates using sequence alignment and structural considerations with emphasis on stem-atom RMSD.
• Benchmark performance: reported RMSDs below 2 Å for loops up to six residues and below 3 Å for loops shorter than ten residues.
• Ranked candidates: generates a top-50 list of ranked loop candidates for selection.
• Sequence homology annotation: highlights sequence homology between template and target sequences for candidate assessment.
• Residue exchange and contact detection: denotes proline or glycine exchanges and potential close contacts between loop candidates and other protein regions.
• TMDET integration: applies the TMDET algorithm to model lipid bilayer expansions and determine loop orientation relative to the membrane.

Scientific Applications:

• Globular protein loop modeling: building and placement of loops in water-soluble proteins using LIP-derived segments.
• Membrane protein loop modeling: modeling membrane protein loops and determining their orientation within lipid bilayers using LIMP and TMDET.
• Structural validation: assessment and benchmarking of loop placements by stem-atom RMSD metrics.
• Sequence-guided loop selection: screening and selection of candidate loops based on sequence criteria and homology.

Methodology:

Searches candidate segments against the LIP and LIMP databases, scores and ranks candidates using sequence alignment and structural considerations focusing on stem-atom RMSD, flags proline/glycine exchanges and potential close contacts, and uses the TMDET algorithm for lipid bilayer modeling.