QUARK

QUARK predicts three-dimensional protein structures from amino acid sequences using ab initio fragment assembly for protein structure modeling.

Key Features:

• Ab initio folding: Performs protein structure prediction solely from amino acid sequences using ab initio approaches.
• Fragment assembly: Assembles tertiary structures using structural motifs extracted from previously solved proteins.
• Gapless-threading: Employs a gapless-threading technique to generate position-specific structure fragments.
• Statistical consistency analysis: Derives position-specific fragments through statistical consistency analysis.
• Distance profiles: Extracts distance profiles from derived fragments for use in structure modeling.
• Torsion angle pairs: Extracts torsion angle pairs from derived fragments as modeling restraints.
• Optimal fragment length: Uses an optimal fragment length of approximately 10 residues for structural assembly.
• Fragment count requirement: Requires at least 100 fragments at each location to achieve optimal assembly.
• Comparative accuracy: Achieves accuracy comparable to machine-learning-based methods, including when using fragments from unrelated proteins.

Scientific Applications:

• Drug discovery: Provides predicted protein structures from sequence data to support research in drug discovery.
• Understanding disease mechanisms: Supplies structural models to assist studies of molecular bases of disease.
• Enzyme design: Generates three-dimensional models that can inform enzyme design and engineering efforts.
• Structural biology: Enables ab initio modeling of protein tertiary structure from sequence data for structural biology research.

Methodology:

Applies gapless-threading to generate position-specific structure fragments; derives fragments via statistical consistency analysis to extract distance profiles and torsion angle pairs; performs fragment assembly using structural motifs from previously solved proteins; uses an optimal fragment length of ~10 residues and at least 100 fragments per location.