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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,...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
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...
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...

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Related Experiment Video

Updated: May 7, 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

Proteome-scale docking: myth and reality.

Didier Rognan

    Drug Discovery Today. Technologies
    |September 21, 2013
    PubMed
    Summary
    This summary is machine-generated.

    Protein-ligand docking predicts molecular interactions but faces challenges in accurately calculating binding energies. Advances enable proteome-wide applications, though predictions require careful interpretation regarding accuracy and completeness.

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    Published on: July 8, 2025

    Related Experiment Videos

    Last Updated: May 7, 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

    Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
    05:08

    Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

    Published on: July 8, 2025

    Area of Science:

    • Computational chemistry
    • Structural biology
    • Pharmacology

    Background:

    • Protein-ligand docking is a key computational tool for predicting molecular interactions.
    • Significant advancements have improved docking speed and the handling of target flexibility.
    • High-resolution protein structures and reliable models facilitate multi-target docking applications.

    Purpose of the Study:

    • To explore the application of protein-ligand docking across multiple targets.
    • To assess the utility of docking for predicting primary and secondary targets of bioactive compounds.
    • To evaluate the potential of docking for drug repurposing.

    Main Methods:

    • Utilized protein-ligand docking simulations.
    • Applied docking to predict interactions with multiple macromolecular targets.
    • Scored and analyzed numerous docking poses for heterogeneous targets.

    Main Results:

    • Docking enables rapid prediction of ligand-target binding.
    • Multi-target docking introduces complexities in pose scoring.
    • Proteome-wide docking shows promise but requires cautious interpretation.

    Conclusions:

    • Protein-ligand docking is a valuable method for predicting molecular interactions, despite limitations in binding free energy calculations.
    • The expansion of docking to multiple targets aids in identifying drug targets and repurposing existing medications.
    • Proteome-wide docking predictions necessitate careful consideration of their recall and precision.