PatchMAN

PatchMAN maps receptor surfaces with structural motifs to perform receptor-centric blind peptide docking and model near-native peptide–protein complexes from free receptor structures.

Key Features:

• Receptor-centric docking: Shifts from peptide-centered methods to a global, receptor-focused peptide-docking approach that samples peptide binding based on receptor structure.
• Backbone-scaffold motif mapping: Maps the receptor surface using backbone scaffolds extracted from protein structures to identify candidate peptide-binding motifs.
• Sequence-independent conformation sampling: Samples bound peptide conformations based solely on the receptor's structural context without relying on peptide sequence information.
• Motif sourcing from monomers and interfaces: Identifies structural units of peptides within both interfaces and monomeric proteins to expand the motif search space.
• High-resolution near-native identification: On a nonredundant set of protein–peptide complexes starting from free receptor structures, identifies near-native complexes within 2.5 Å/5 Å interface backbone RMSD in 58%/84% of cases and achieves corresponding sampling in 81%/100% of instances.
• Patch-Motif AligNments: Leverages motif alignments (Patch-Motif AligNments) to match receptor surface patches to peptide backbone scaffolds.

Scientific Applications:

• Peptide–protein interaction modeling: Enables modeling of bound peptide conformations and orientations at high resolution.
• Peptide binder design: Provides structural templates and binding modes to inform design of novel peptide binders.
• Mechanistic studies: Facilitates analysis of the principles underlying peptide recognition and peptide–protein associations.

Methodology:

Implements a global, receptor-centric docking approach that maps receptor surfaces using structural motifs and backbone scaffolds extracted from protein structures, samples peptide conformations based on receptor structural context, and identifies near-native complexes assessed by interface backbone RMSD (2.5 Å and 5 Å) starting from free receptor structures.