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Related Concept Videos

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-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...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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,...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Factors Affecting Protein-Drug Binding: Drug-Related Factors01:18

Factors Affecting Protein-Drug Binding: Drug-Related Factors

Drug binding to proteins is a complex phenomenon influenced by various drug-related factors, each playing a significant role in the interaction between drugs and proteins within the body.
One crucial factor in drug-protein binding is the drug's lipophilicity or its affinity for fat. More lipophilic drugs tend to have higher binding extents. For example, highly lipophilic drugs like cloxacillin exhibit substantial protein binding, with as much as 95% of the drug binding to proteins. In contrast,...

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Related Experiment Video

Updated: Jul 9, 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

NPBIP: predicting binding preferences of uncharacterized nucleic-acid-binding proteins.

Noam Shimshoviz1, Safwan Butto2, Yaron Orenstein1,2

  • 1The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel.

Bioinformatics (Oxford, England)
|July 7, 2026
PubMed
Summary

A new computational method, NPBIP, accurately predicts nucleic-acid-binding protein (NBP) interactions with RNA and DNA. This tool overcomes limitations of existing methods by integrating similarity and deep learning approaches for enhanced binding affinity predictions.

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An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • Nucleic-acid-binding proteins (NBPs) regulate gene expression by recognizing specific DNA or RNA sequences.
  • Predicting NBP binding affinities for novel sequences is challenging due to limitations in current computational methods.
  • Existing tools often require query-specific experimental data or are restricted to short sequence predictions.

Purpose of the Study:

  • To develop a novel computational method for predicting the binding affinity of any query NBP to any RNA or DNA sequence.
  • To overcome the limitations of existing methods that require prior experimental data or are restricted to short sequences.
  • To provide a robust and accurate tool for NBP-DNA and NBP-RNA interaction prediction.

Main Methods:

  • Integration of a similarity-based method and a deep-learning model (large protein language model with a hybrid convolutional-transformer network).
  • Training and evaluation on 420 RNA-binding protein (RBP) and 464 DNA-binding protein (DBP) experiments.
  • Utilizing publicly available source code and datasets for reproducibility.

Main Results:

  • The New Protein Binding Intensity Predictor (NPBIP) significantly outperformed its individual components and competing baselines.
  • Achieved mean Pearson correlations of 0.414±0.20 for RNA-binding and 0.581±0.22 for DNA-binding experiments.
  • Demonstrated biological validation through recovery of canonical binding motifs for both RBPs and DBPs.

Conclusions:

  • NPBIP offers a significant advancement in predicting NBP binding affinities across diverse nucleic acid sequences.
  • The method provides statistically comparable or superior performance to experimental upper bounds.
  • Interpretability analysis confirms the biological relevance of NPBIP's predictions.