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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...
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 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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Related Experiment Video

Updated: Jun 6, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

A holistic molecular docking approach for predicting protein-protein complex structure.

XinQi Gong1, Bin Liu, Shan Chang

  • 1College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.

Science China. Life Sciences
|November 25, 2010
PubMed
Summary

A new protein-protein docking method, HoDock, accurately predicts complex structures. It correctly identified key binding residues and generated high-quality models, showing promise for improving protein complex structure prediction.

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Last Updated: Jun 6, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

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Protein Target Prediction and Validation of Small Molecule Compound
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Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Molecular Modeling

Background:

  • Protein-protein interactions are crucial for cellular functions.
  • Accurate prediction of protein complex structures is essential for understanding biological mechanisms.

Purpose of the Study:

  • To introduce and validate a novel holistic protein-protein molecular docking approach, HoDock.
  • To assess the performance of HoDock using CAPRI Target 39.

Main Methods:

  • HoDock integrates binding site prediction, complex structure sampling, clustering, scoring, and selection.
  • The approach was applied to CAPRI Target 39 for structure prediction.

Main Results:

  • HoDock correctly predicted three key binding site residues (A191HIS, B512ARG, B531ARG).
  • Five submitted structures achieved a high fraction of correct receptor-ligand interface residues.
  • The method demonstrated potential for enhanced prediction accuracy in protein complex structures.

Conclusions:

  • The established HoDock approach shows efficacy in predicting protein-protein complex structures.
  • This method may offer improvements in accuracy for structural bioinformatics and drug discovery.