Proceedings of the National Academy of Sciences of the United States of America
Dec 22, 2025
We describe peptide mapping through Split Antibiotic Resistance Complementation (SpARC-map), a method to identify the probable interface between two interacting proteins. Our method is based on in vivo affinity selection inside a bacterial host and u...
Predicting protein‒protein interactions (PPIs) plays a crucial role in understanding biological processes. Although biological experimental methods can identify PPIs, they are costly, time-consuming, labor-intensive, and often lack stability. In cont...
Protein-protein interactions (PPIs) are essential for biological function. Coevolutionary analysis and deep-learning (DL)-based protein structure prediction have enabled comprehensive PPI identification in bacteria and yeast, but these approaches hav...
BACKGROUND: The identification of protein-protein interaction (PPI) plays a crucial role in understanding the mechanisms of complex biological processes. Current research in predicting PPI has shown remarkable progress by integrating protein informat...
Journal of chemical information and modeling
Oct 10, 2025
Phosphorylation dynamically orchestrates the protein-protein interaction (PPI) network that governs cellular signaling, and its dysregulation frequently drives malignant transformation and neurodegeneration. We present PhosPPI-SEQ, an interpretable d...
Intrinsically disordered proteins and regions (IDRs) lack stable 3D structures, posing challenges for interaction prediction. We present SpatPPI, a geometric deep learning model tailored for IDPPI prediction. SpatPPI leverages structural cues from fo...
Journal of chemical information and modeling
Sep 19, 2025
Protein-protein interactions (PPIs) play fundamental roles in biological processes and therapeutic development. Accurately predicting PPI binding affinity is critical for understanding interaction mechanisms and guiding protein engineering. Recent ad...
Molecular interaction networks are a vital tool for studying biological systems. While many tools exist that visualize a protein or a pathway within a network, no tool provides the ability for a researcher to consider a protein's position in a networ...
, a widespread human parasite, persists in hosts through complex molecular interactions. Protein-protein interactions (PPIs) underpin essential biological processes, including parasite-host interactions and cellular invasion. Herein, we utilized adva...
BACKGROUND: Protein-protein interactions (PPIs) play a critical role in essential biological processes such as signal transduction, enzyme activity regulation, cytoskeletal structure, immune responses, and gene regulation. However, current methods ma...
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