STRIKE

STRIKE evaluates and compares alternative multiple protein sequence alignments by using structural information derived from a single protein structure to assess alignment accuracy.

Key Features:

• Single Structure Utilization: Uses a single protein structure to assess and compare different multiple sequence alignments for the same set of sequences.
• Accuracy Assessment: Determines the relative accuracy of two alternative alignments by applying refined definitions of contacts and an improved contact substitution score.
• Validation on Reference Datasets: Has been validated on BAliBASE, Homestrad, and Prefab reference datasets.
• Performance Metrics: Identifies the more accurate alignment in ~70% of cases overall and ~79% for challenging datasets such as the RV11 category in BAliBASE, showing superior discrimination compared to metrics like Contact Accepted mutation or Blosum.

Scientific Applications:

• Limited-structure alignment assessment: Enables evaluation of multiple sequence alignments when only a single protein structure is available.
• Evolutionary biology: Supports comparative analyses that require accurate alignments informed by structural contacts.
• Protein engineering: Informs selection of accurate alignments for downstream structure-based design and mutation interpretation.
• Functional genomics: Aids interpretation of sequence-function relationships by improving alignment accuracy relative to known structures.

Methodology:

Refines contact definitions and employs an enhanced contact substitution score to evaluate and compare alternative alignments using a single protein structure.