PredUs

PredUs predicts protein-protein interfaces using three-dimensional structural information by mapping interfacial contacts from structurally similar proteins onto a query structure and scoring surface residues to identify likely interface sites.

Key Features:

• Interface mapping: Maps interfacial contacts from known interfaces of structurally similar proteins onto surface residues of the query protein.
• Structural neighbor exploitation: Uses both close and remote structural neighbors to exploit conservation of binding sites across protein structure space.
• Support vector machine scoring: Employs a support vector machine to compute per-residue scores indicating the likelihood of being part of an interface.
• Three-dimensional structural information: Leverages query protein 3D structure to transfer interface contacts and detect conserved interface patterns.

Scientific Applications:

• Protein-protein interaction prediction: Predicts whether two proteins form a complex by identifying likely interfacial residues on a query structure.
• Functional site inference: Provides insights into functional aspects of proteins and conserved binding sites that may not be apparent from sequence analysis alone, supporting studies of cellular processes and disease mechanisms.

Methodology:

Maps contacts from known interfaces of close and remote structural neighbors onto query protein surface residues and applies a support vector machine to score each residue, based on the principle of interface conservation across protein structure space.