(PS)2 - v3

(PS)2 - v3 predicts three-dimensional structures of protein complexes and analyzes coupling between subunits by combining comparative modeling with structural and evolutionary profile analyses.

Key Features:

• Comparative Modeling Approach: Employs PSI-BLAST and IMPALA for template selection and T-Coffee for target–template alignment to produce consensus alignments.
• Structure Prediction: Builds three-dimensional models of protein complexes using MODELLER based on selected templates and alignments.
• Subunit Coupling Analysis: Integrates structural and evolutionary considerations to assess coupling between subunits and infer effects on complex stability and function.
• Profile Comparison: Compares structural and evolutionary profiles of each subunit with and without packing contributions from other subunits to indicate monomeric versus complex preference.

Scientific Applications:

• Molecular basis of protein function: Investigates how structural features and subunit interactions determine protein function.
• Protein–protein interactions: Analyzes inter-subunit coupling to inform studies of interaction specificity and interface properties.
• Structural dynamics of complexes: Assesses how packing and evolutionary signals relate to preferred biological states of subunits within complexes.
• Hypothesis generation: Supports generation of hypotheses about subunit coupling and its impact on complex stability and functionality.

Methodology:

Initial sequence searches and template selection use PSI-BLAST and IMPALA, alignments are refined with T-Coffee, final models are built with MODELLER, and subunit coupling is evaluated via structural and evolutionary profile comparisons with and without packing contributions.