InterEvol

InterEvol catalogs 3D structures of binding interfaces from homologous protein complexes and provides interolog identification and multiple sequence alignments to study the evolution of protein–protein interactions.

Key Features:

• Identification of Structural Interologs: For each chain forming a complex in the Protein Data Bank (PDB), InterEvol identifies close and remote structural interologs to capture evolutionary snapshots of protein interfaces.
• Structure Retrieval and Visualization: Tools for retrieval and visualization of structures enable examination of binding interfaces and their structural variation across interologs.
• Pre-computed Multiple Sequence Alignments (MSAs): Pre-computed MSAs are provided for most likely interologs across a diverse range of species.
• Flexible Query Options: The database supports queries via PDB code, keywords, or sequences of one or two interacting partners.
• InterEvolAlign Recomputed MSAs: InterEvolAlign allows recomputation of multiple sequence alignments with tailored parameters for specific interolog sets.
• PyMol Integration: An InterEvol PyMol plugin integrates structural views with sequence alignments at protein interfaces.

Scientific Applications:

• Interface evolution analysis: Comparative analysis of interologs and MSAs to investigate evolutionary trajectories of protein–protein interfaces.
• Structural characterization of interactions: Examination of 3D interface geometries and conformational variation across homologous complexes.
• Cross-species comparative studies: Use of interologs and MSAs to compare interaction conservation and divergence across diverse species.
• Interface-focused drug discovery: Structural and evolutionary information to inform targeting of protein–protein interfaces in drug design.

Methodology:

Automated methods extract and curate structural and sequence data from PDB entries, automatically identify structural interologs for complex chains, and generate pre-computed multiple sequence alignments; InterEvolAlign performs recomputation of MSAs with user-specified parameters.