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

Structure-Activity Relationships and Drug Design01:28

Structure-Activity Relationships and Drug Design

Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence its...
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.
Viral Structure00:56

Viral Structure

Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
G Protein-coupled Receptors01:15

G Protein-coupled Receptors

G Protein-Coupled Receptors or GPCRs are membrane-bound receptors that transiently associate with heterotrimeric G proteins and induce an appropriate response to sensory stimuli such as light, odors, hormones, cytokines, or neurotransmitters.
GPCRs are also called heptahelical, 7TM, or serpentine receptors, and consist of seven (H1-H7) transmembrane alpha-helices that span the bilayer to form a cylindrical core. The transmembrane helices are connected by three extracellular loops and three...
Drug Discovery: Overview01:26

Drug Discovery: Overview

Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...

You might also read

Related Articles

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

Sort by
Same author

Design, synthesis and biological activity of glycoconjugated ADAMTS5 exosite inhibitors: applications in osteoarthritis and ovarian cancer models.

Scientific reports·2025
Same author

Improving Machine Learning Classification Predictions through SHAP and Features Analysis Interpretation.

Journal of chemical information and modeling·2025
Same author

Design, synthesis, and biological evaluation of chalcone derivatives as selective Monoamine Oxidase-B inhibitors with potential neuroprotective effects.

European journal of medicinal chemistry·2025
Same author

Structure-Based Discovery of Hsp90/HDAC6 Dual Inhibitors Targeting Aggressive Prostate Cancer.

Journal of medicinal chemistry·2025
Same author

Selective imaging probes for differential detection of pathological tau polymorphs in tauopathies.

Drug discovery today·2025
Same author

Exploring Biological Targets of Magnolol and Honokiol and their Nature-Inspired Synthetic Derivatives: In Silico Identification and Experimental Validation of Estrogen Receptors.

Journal of natural products·2024
Same journal

Sustained Intra-Articular Delivery of Triple Therapeutics Using a Phase-Transition Phospholipid-Based Gel for Effective Treatment of Gouty Arthritis.

Pharmaceutical research·2026
Same journal

Spray Dried Lysozyme Microspheres: Morphological Evolution and Enzymatic Activity Retention.

Pharmaceutical research·2026
Same journal

Colloidal Stability of Amorphous Nanoparticles in Solution: Impact of Stabilizer.

Pharmaceutical research·2026
Same journal

Impact of Mixing Approach and Bubble Formation on In Situ Forming Implant Properties.

Pharmaceutical research·2026
Same journal

Initial Exploration on the Application of the MoCMC Approach for Determining In Vitro Product Comparability.

Pharmaceutical research·2026
Same journal

Injectable in-situ Forming Lipid Liquid Crystal for Long-acting Fluocinolone Release in Posterior Ocular Therapy: In-vitro and In-vivo Evaluations.

Pharmaceutical research·2026
See all related articles

Related Experiment Video

Updated: May 13, 2026

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
08:35

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Emerging topics in structure-based virtual screening.

Giulio Rastelli1

  • 1Life Sciences Department, University of Modena and Reggio Emilia, Via Campi 183, 41125, Modena, Italy. giulio.rastelli@unimore.it

Pharmaceutical Research
|March 8, 2013
PubMed
Summary
This summary is machine-generated.

Molecular dynamics simulations and custom chemical libraries enhance structure-based virtual screening by addressing target flexibility, improving the drug discovery pipeline.

More Related Videos

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

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Related Experiment Videos

Last Updated: May 13, 2026

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
08:35

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

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

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Molecular modeling

Background:

  • Structure-based virtual screening (SBVS) is crucial for identifying drug candidates.
  • Target flexibility presents a significant challenge in traditional SBVS.
  • Advancements in computational methods are needed to overcome these limitations.

Purpose of the Study:

  • To discuss the growing importance of molecular dynamics simulations in SBVS.
  • To highlight the role of generating custom chemical libraries for drug discovery.
  • To provide perspective on integrating these computational approaches into the drug discovery pipeline.

Main Methods:

  • Review of molecular dynamics (MD) simulations for assessing protein flexibility.
  • Discussion on the strategic generation of targeted, in-house chemical libraries.
  • Analysis of how these methods complement and enhance traditional SBVS.

Main Results:

  • MD simulations effectively capture target dynamics, improving screening accuracy.
  • Custom libraries can be tailored to specific binding site features, increasing hit rates.
  • Integrating MD and library generation optimizes lead identification and reduces attrition.

Conclusions:

  • Molecular dynamics simulations and custom chemical library generation are vital for modern structure-based virtual screening.
  • These computational strategies significantly improve the treatment of target flexibility.
  • Adoption of these methods enhances the efficiency and success rate of the drug discovery pipeline.