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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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...

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Related Experiment Video

Updated: Jun 16, 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

SPPIDER-seq: Sequence-based Partner-aware Predictor of Protein-Protein Interaction Sites.

Aleksey Porollo1, Om Jadhav2, Aaron Alvarez2

  • 1Department of Biostatistics, Health Informatics and Data Sciences, the University of Cincinnati College of Medicine, Cincinnati, OH, USA 45267.

Bioinformatics (Oxford, England)
|June 15, 2026
PubMed
Summary
This summary is machine-generated.

SPPIDER-seq is a new framework for predicting protein-protein interaction (PPI) sites by considering partner context. It outperforms existing methods on disordered interfaces and reveals partner-specific binding patterns.

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Last Updated: Jun 16, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Interaction Networks

Background:

  • Traditional protein-protein interaction (PPI) site predictors often ignore crucial partner-specific context, especially for transient and disordered interactions.
  • Interface specificity is vital for understanding biological recognition, particularly in dynamic and intrinsically disordered protein systems.

Purpose of the Study:

  • To develop a partner-aware PPI site prediction framework that incorporates interacting partner information.
  • To improve the accuracy of predicting interaction sites, especially for challenging disordered and transient protein complexes.

Main Methods:

  • Introduced SPPIDER-seq, a novel framework utilizing pretrained ESM-2 embeddings and a cross-attention architecture.
  • Developed two complementary models: a receptor-centric model for structured interfaces and a peptide-centric model for disordered, motif-driven binding.
  • Trained and benchmarked models on curated, non-redundant protein-peptide interaction datasets from BioLiP.

Main Results:

  • SPPIDER-seq achieved high performance on blind benchmarks, with AUROC up to 0.797 and MCC up to 0.269.
  • Outperformed AlphaFold3 on peptide-mediated and disordered interfaces, demonstrating complementary performance on globular complexes.
  • Analysis of 341 TP53 interaction partners revealed distinct, partner-specific interface patterns in both structured and disordered regions.

Conclusions:

  • SPPIDER-seq effectively captures partner-specific context for accurate PPI site prediction, particularly for disordered interactions.
  • The framework provides insights into the molecular basis of protein recognition across different interface types.
  • SPPIDER-seq models, datasets, and code are publicly available, facilitating further research in protein interaction prediction.