partiFold

partiFold performs simultaneous alignment and consensus folding of unaligned protein sequences to analyze folding landscapes of transmembrane beta-barrel (TMB) proteins, with emphasis on low-sequence-homology cases.

Key Features:

• Simultaneous Alignment and Folding: Integrates sequence alignment with consensus folding in a single computational step for unaligned, low-homology proteins.
• Polynomial Complexity: Operates with polynomial time and space complexity.
• Exploitation of Structural Sparsity: Leverages sparsity in super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time.
• Comparative Performance: Demonstrated superior performance versus structurally derived sequence alignments, particularly in low-sequence-homology TMB cases.

Scientific Applications:

• TMB Folding Landscape Analysis: Facilitates exploration and consensus folding of transmembrane beta-barrel protein folding landscapes to aid prediction and interpretation of structural configurations.
• Low-Homology Structure Prediction: Applies to other protein families with sparse structural pairings where traditional sequence-alignment-based structure prediction is challenging.

Methodology:

Uses an algorithmic approach that focuses on super-secondary structures and leverages sparsity in structure pairings and alignment candidates to perform simultaneous alignment and consensus folding with polynomial time and space complexity.