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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...

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Related Experiment Video

Updated: Jul 12, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Pep2Mol: 3D Molecule Generation Targeting Protein-Protein Interfaces with Diffusion Models.

Rongting Yue, Zekun Yang, Gustavo Seabra

    Biorxiv : the Preprint Server for Biology
    |July 10, 2026
    PubMed
    Summary

    Pep2Mol designs small molecules to target protein-protein interactions (PPIs) by using peptide or protein structures for guidance. This novel approach generates effective drug candidates for challenging PPI targets.

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    Published on: December 25, 2021

    Area of Science:

    • Computational biology
    • Drug discovery
    • Structural biology

    Background:

    • Protein-protein interactions (PPIs) are crucial for biological functions.
    • Targeting PPIs offers a promising strategy for developing therapeutics against previously undruggable proteins.
    • Current structure-based drug design methods are limited in addressing the complex interfaces of PPIs.

    Purpose of the Study:

    • To introduce Pep2Mol, a novel diffusion-based generative model for designing small molecules against PPIs.
    • To overcome limitations of conventional pocket-centric drug design by incorporating protein structural information.
    • To enable the design of inhibitors for challenging, large, and shallow PPI interfaces.

    Main Methods:

    • Development of Pep2Mol, a generative model utilizing SE(3)-equivariant graph neural networks.
    • Integration of protein-ligand and protein-peptide interaction encoding with attention-based conditioning.
    • Curation of a dataset comprising 10,956 experimentally resolved protein complex structure pairs.

    Main Results:

    • Pep2Mol successfully generates chemically valid small molecules.
    • Generated molecules exhibit state-of-the-art binding affinities against PPI targets.
    • The model demonstrates superior performance in designing ligands for orthosteric PPI sites.

    Conclusions:

    • Pep2Mol represents a significant advancement in structure-based drug design for PPIs.
    • The model provides a robust framework for developing small-molecule inhibitors against challenging protein interfaces.
    • This approach broadens the scope of druggable targets by enabling modulation of PPIs.