Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

pH Sensitivity of the SERF1a Conformational Ensemble.

ACS omega·2026
Same author

Biomimetic affinity sensor for the ultrasensitive detection of neonicotinoids.

Biosensors & bioelectronics·2023
Same author

Low-resolution description of the conformational space for intrinsically disordered proteins.

Scientific reports·2022
Same author

A Curvilinear-Path Umbrella Sampling Approach to Characterizing the Interactions Between Rapamycin and Three FKBP12 Variants.

Frontiers in molecular biosciences·2022
Same author

The effect of different colored light emitting diode illumination on egg laying performance, egg qualities, blood hormone levels and behavior patterns in Brown Tsaiya duck.

Animal bioscience·2021
Same author

Quantitative phosphoproteomic analysis identifies the potential therapeutic target EphA2 for overcoming sorafenib resistance in hepatocellular carcinoma cells.

Experimental & molecular medicine·2020
Same journal

Exploration of a Novel Physicochemical Property Space for the Development of Antimalarial Drugs.

Current topics in medicinal chemistry·2026
Same journal

Computational Drug Design of Natural Product-Based Azole Hybrids for Multifactorial Diseases: Success Stories.

Current topics in medicinal chemistry·2026
Same journal

Simulated Natural Nanoparticles in Bai-Hu-Tang Decoction: Preparation, Characterization, Pharmacokinetics, and Antipyretic Effects.

Current topics in medicinal chemistry·2026
Same journal

Dolabellane Diterpenes from the Marine Brown Alga Dictyota dolabellana and their Potential Antiviral Activity.

Current topics in medicinal chemistry·2026
Same journal

Inhibitory Effects of Flavonoids from the Stems and Leaves of Scutellaria baicalensis Georgi on Oligodendrocyte Pyroptosis Induced by Aβ1-42.

Current topics in medicinal chemistry·2026
Same journal

Mechanism of Huangqishihu Decoction in Treating Liver Fibrosis in Rats Model via Regulation of Oxidative Stress and Nrf2 Signaling Pathway.

Current topics in medicinal chemistry·2026
See all related articles

Related Experiment Video

Updated: Jun 8, 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

Accommodating protein flexibility for structure-based drug design.

Jung-Hsin Lin1

  • 1Division of Mechanics, Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan. jhlin@gate.sinica.edu.tw

Current Topics in Medicinal Chemistry
|October 14, 2010
PubMed
Summary
This summary is machine-generated.

Incorporating protein flexibility is crucial for accurate computational drug design, improving predictions of how small compounds bind to proteins and their affinities. This review explores methods for generating protein ensembles and assessing docking algorithms and scoring functions.

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Related Experiment Videos

Last Updated: Jun 8, 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

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Computational drug design
  • Structural bioinformatics
  • Molecular modeling

Background:

  • Protein flexibility is increasingly recognized as critical for accurate predictions in computational drug design.
  • Existing methods for incorporating protein flexibility in binding predictions have varying successes and limitations.
  • Efficiently generating protein conformation ensembles is key to improving binding mode and affinity predictions.

Purpose of the Study:

  • To review the significance of protein flexibility in predicting ligand binding poses and affinities.
  • To compare various approaches for generating protein conformation ensembles, focusing on efficiency and applicability.
  • To analyze different docking algorithms, scoring functions, and free energy calculation methods.

Main Methods:

  • Review of existing literature on protein flexibility in computational drug design.
  • Comparison of methods for generating protein conformation ensembles.
  • Analysis of docking search algorithms and scoring functions.
  • Brief review of end-point free energy calculation methods (MM/PBSA, LIE).

Main Results:

  • Protein flexibility significantly impacts the accuracy of binding pose and affinity predictions.
  • Various ensemble generation techniques offer different trade-offs between accuracy and computational cost.
  • The choice of docking algorithm and scoring function is crucial for reliable predictions.
  • End-point free energy methods provide valuable insights into binding affinities.

Conclusions:

  • Incorporating protein flexibility is essential for advancing computational drug design.
  • Selecting appropriate methods for ensemble generation and docking is key to successful drug discovery.
  • Further development in algorithms and scoring functions can enhance prediction accuracy.
  • The review provides a framework for understanding and applying protein flexibility in drug design.