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Related Concept Videos

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...
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...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in 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...

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Related Experiment Video

Updated: Jun 4, 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

Bio-inspired algorithms applied to molecular docking simulations.

G Heberlé1, W F de Azevedo

  • 1Faculdade de Biociências, Laboratório de Bioquímica Estrutural, Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Nacional de Ciência e Tecnologia em Tuberculose-Pontifícia Universidade Católica do Rio Grande do Sul, CEP 90619-900, Porto Alegre - RS, Brazil.

Current Medicinal Chemistry
|March 4, 2011
PubMed
Summary

Biologically inspired algorithms (BIAs) mimic nature for computational drug discovery. This review details BIAs, focusing on evolutionary algorithms for protein-ligand docking simulations, particularly against Mycobacterium tuberculosis targets.

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Last Updated: Jun 4, 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

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
  • Bioinformatics
  • Drug discovery

Background:

  • Nature inspires novel computational methods, including biologically inspired algorithms (BIAs).
  • BIAs simulate biological systems for computational paradigms like neural networks, evolutionary computing, and swarm intelligence.
  • Molecular docking is crucial for analyzing protein-ligand interactions in drug discovery.

Purpose of the Study:

  • To review the core concepts of BIAs applied to molecular docking simulations.
  • To highlight specific evolutionary algorithms (EAs) used in this context.
  • To present recent applications of BIAs targeting Mycobacterium tuberculosis proteins.

Main Methods:

  • Review of biologically inspired algorithms (BIAs).
  • Focus on evolutionary computing, including guided-directed and Lamarckian genetic algorithms.
  • Application analysis of BIAs in molecular docking simulations.

Main Results:

  • BIAs offer powerful approaches for simulating protein-ligand interactions.
  • Evolutionary algorithms demonstrate significant utility in molecular docking.
  • These methods show promise for identifying drug targets in Mycobacterium tuberculosis.

Conclusions:

  • BIAs provide effective computational strategies for drug discovery.
  • Evolutionary algorithms are particularly well-suited for molecular docking.
  • The application of BIAs to Mycobacterium tuberculosis targets represents a significant advancement in combating the disease.