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

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...
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 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...
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...
Membrane Fluidity01:26

Membrane Fluidity

Membrane fluidity is explained by the fluid mosaic model of the cell membrane, which describes the plasma membrane structure as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character.
Mosaic nature of the membrane
The mosaic characteristic of the membrane helps the plasma membrane remain fluid. The integral proteins and lipids exist as separate but loosely-attached molecules in the membrane. The membrane is a relatively...

You might also read

Related Articles

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

Sort by
Same author

A workflow to create a high-quality protein-ligand binding dataset for training, validation, and prediction tasks.

Digital discovery·2025
Same author

A Workflow to Create a High-Quality Protein-Ligand Binding Dataset for Training, Validation, and Prediction Tasks.

ArXiv·2025
Same author

Discovery of DNL343: A Potent, Selective, and Brain-Penetrant eIF2B Activator Designed for the Treatment of Neurodegenerative Diseases.

Journal of medicinal chemistry·2024
Same author

Rescue of a lysosomal storage disorder caused by Grn loss of function with a brain penetrant progranulin biologic.

Cell·2024
Same author

Author Correction: CD98hc is a target for brain delivery of biotherapeutics.

Nature communications·2023
Same author

CD98hc is a target for brain delivery of biotherapeutics.

Nature communications·2023
Same journal

Lasing emission spectroscopy for bioanalytics and biomedicine.

Quarterly reviews of biophysics·2026
Same journal

Elementary processes and mechanisms of nanopore formation induced by antimicrobial peptides and other membrane-active peptides.

Quarterly reviews of biophysics·2026
Same journal

Biomineralization: Perspectives on control of crystal polymorphism, order-disorder and solvation states.

Quarterly reviews of biophysics·2026
Same journal

The pivotal roles of cellular biophysics and mechanobiology in the development of Human Organs-on-Chips.

Quarterly reviews of biophysics·2026
Same journal

Biophysics meets fungal biology: Characterising the fungal cell envelope and its interactions with drug-like molecules.

Quarterly reviews of biophysics·2026
Same journal

Energy landscapes in molecular biology: History, principles, and perspectives.

Quarterly reviews of biophysics·2026
See all related articles

Related Experiment Video

Updated: May 22, 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 flexibility in docking and surface mapping.

Katrina W Lexa1, Heather A Carlson

  • 1Department of Medicinal Chemistry, University of Michigan, Ann Arbor, 48109-1065, USA.

Quarterly Reviews of Biophysics
|May 10, 2012
PubMed
Summary
This summary is machine-generated.

Flexible protein-ligand docking improves drug discovery by accounting for protein movement. This review explores methods, limitations, and future directions for more accurate drug design.

Related Experiment Videos

Last Updated: May 22, 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

Area of Science:

  • Computational chemistry
  • Structural biology
  • Pharmacology

Background:

  • Structure-based drug design is crucial for identifying and refining drug candidates.
  • Protein flexibility is vital for accurately representing the native state, yet often overlooked in docking.
  • Current rigid receptor docking methods have limited accuracy (50-75%).

Purpose of the Study:

  • To review current computational tools for flexible protein-ligand docking.
  • To discuss receptor surface mapping techniques.
  • To identify limitations and future prospects in flexible docking.

Main Methods:

  • Examination of existing literature on flexible docking algorithms.
  • Analysis of receptor surface mapping methodologies.
  • Discussion of computational approaches for modeling protein dynamics.

Main Results:

  • Fully flexible docking methods can significantly enhance pose prediction accuracy (80-95%).
  • Acknowledging protein flexibility is key to improving docking performance.
  • Various computational tools are available for flexible docking and surface analysis.

Conclusions:

  • Flexible protein-ligand docking offers superior accuracy over rigid methods.
  • Further development in flexible docking is essential for advancing drug discovery.
  • Future research should focus on enhancing computational efficiency and accuracy.