FoldMason

FoldMason performs fast multiple structural alignment of protein structures to analyze conserved three-dimensional conformations among distantly related proteins.

Key Features:

• Progressive multiple structural alignment: A progressive MSTA method capable of aligning hundreds of thousands of protein structures.
• Foldseek 3Di structural alphabet: Leverages Foldseek's 3Di structural alphabet and its pairwise structural alignment approach to represent and compare protein conformations.
• High speed: Achieves alignments two orders of magnitude faster than existing MSTA methods while maintaining or exceeding alignment quality.
• Confidence scoring: Computes confidence scores for alignments to quantify reliability.
• Large-scale analysis support: Designed for large-scale protein-structure analyses enabled by recent accurate structural prediction methods.

Scientific Applications:

• Flaviviridae glycoprotein phylogenetics: Applied to Flaviviridae glycoproteins to support phylogenetic analysis using structural conservation below the sequence twilight zone.

Methodology:

Progressive multiple structural alignment using Foldseek's 3Di structural alphabet and pairwise structural alignment information, with computation of per-alignment confidence scores.