cpxDeepMSA

cpxDeepMSA generates high-quality multiple sequence alignments (MSAs) for protein complexes to enable analysis of coevolutionary relationships and inter-protein residue contacts in protein-protein interactions (PPIs).

Key Features:

• Deep Cascade Algorithm: Employs a deep cascade algorithm that integrates multiple strategies to improve the depth, sensitivity, and robustness of protein complex MSAs.
• Integration of Diverse Strategies: Combines genomic distance, phylogeny information, and the STRING interaction network to join monomer MSA results into a comprehensive protein complex MSA (cpxMSA), mitigating failure modes of single-method joining for two-monomer MSAs.
• Wide Range of Sequence Sources: Utilizes multiple protein monomer databases as sequence sources for constructing monomer MSAs used in complex assembly.
• Strong Generalization Ability: Designed to generalize across diverse datasets and types of protein complexes to produce consistent MSA results.

Scientific Applications:

• Protein Complex Structure Predictions: Provides MSAs that support prediction of three-dimensional structures of protein complexes.
• Inter-Protein Residue-Residue Contacts Prediction: Supports prediction of contacts between residues of interacting proteins for mapping PPI interfaces.
• Biological Sequence Coevolution Analysis: Enables coevolutionary analysis by supplying MSAs that capture evolutionary coupling within and between protein partners.

Methodology:

Applies a deep cascade algorithm that integrates genomic distance, phylogeny information, and the STRING interaction network to join monomer MSAs from protein monomer databases into a comprehensive protein complex MSA (cpxMSA).