THREADER

THREADER performs protein fold recognition by threading amino acid side chains onto pre-existing backbone structures and evaluating three-dimensional conformations using pair potentials and a solvation potential.

Key Features:

• Threading / Fold recognition: Implements threading (fold recognition) to assign protein folds based on sequence-to-structure fits.
• Three-dimensional modeling: Threads sequences of amino acid side chains onto pre-existing backbone structures (folds) to generate 3-D conformations.
• Scoring functions: Evaluates proposed 3-D conformations using a combination of pair potentials and a distinct solvation potential.
• Alignment analysis: Analyzes threading alignments to detect partial rather than whole-fold matching.
• Z-score assessment: Considers pairwise energy and solvation energy Z-scores for assessing candidate folds.
• Benchmarking: Demonstrated correct fold assignments for 7 out of 11 chains in a blind testing experiment.

Scientific Applications:

• Protein fold prediction: Predicts and assigns protein folds using threading-based evaluation and scoring functions, as shown by blind-test results.
• Partial fold recognition: Identifies partial fold components, exemplified by recognition of (alpha beta)8 barrels based on constituent parts.
• Fold validation and scoring: Validates candidate folds through pair potentials, a solvation potential, and Z-score comparisons.

Methodology:

Performs threading (fold recognition) by threading amino acid side chains onto backbone structures, evaluates 3-D conformations with pair potentials and a solvation potential, analyzes threading alignments, and assesses candidates using pairwise energy and solvation energy Z-scores.