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

789
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...
789
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
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...
4.2K
Ligand Binding Sites02:40

Ligand Binding Sites

7.8K
7.8K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

13.0K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
13.0K

You might also read

Related Articles

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

Sort by
Same author

Corrigendum to "Dioscorea polystachya Turcz. Extract attenuates osteoclastogenesis and ovariectomy-induced bone loss in rats" [J. Ethnopharmacol. 356 (2026) 120833].

Journal of ethnopharmacology·2026
Same author

Dioscorea polystachya Turcz. Extract attenuates osteoclastogenesis and ovariectomy-induced bone loss in rats.

Journal of ethnopharmacology·2025
Same author

Structural basis for sirtuin 2 activity and modulation: Current state and opportunities.

The Journal of biological chemistry·2025
Same author

Computational Approaches to Predict Hepatitis B Virus Capsid Protein Mutations That Confer Resistance to Capsid Assembly Modulators.

Viruses·2025
Same author

Single-molecule FRET-based approach for protein-targeted drug discovery.

Molecules and cells·2024
Same author

Drugs Targeting Sirtuin 2 Exhibit Broad-Spectrum Anti-Infective Activity.

Pharmaceuticals (Basel, Switzerland)·2024

Related Experiment Video

Updated: Jul 24, 2025

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
09:19

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

3.3K

BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation.

Daniel R Bryan1, John L Kulp1,2, Manoj K Mahapatra3

  • 1Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States.

Journal of Chemical Information and Modeling
|July 5, 2023
PubMed
Summary
This summary is machine-generated.

Fragment-based drug design (FBDD) is now accessible via the BMaps web application, simplifying the process of assembling new drug molecules from protein-binding fragment data. This tool democratizes FBDD by providing precomputed data and user-friendly interfaces for drug discovery programs.

More Related Videos

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

5.1K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.5K

Related Experiment Videos

Last Updated: Jul 24, 2025

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
09:19

NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Published on: June 4, 2021

3.3K
Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

5.1K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.5K

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Structural biology

Background:

  • Fragment-based drug design (FBDD) leverages protein-fragment binding data to create novel therapeutics.
  • Traditional FBDD methods rely on complex simulations and design tools, limiting broader accessibility.
  • Preclinical drug programs have benefited from FBDD, but wider adoption has been hindered by resource requirements.

Purpose of the Study:

  • To develop a user-friendly web application, BMaps, for democratizing fragment-based drug design.
  • To provide researchers with easy access to a comprehensive repository of precomputed fragment-protein binding data.
  • To integrate conventional drug design tools with FBDD in an automated platform.

Main Methods:

  • Developed the BMaps web application with simplified user interfaces.
  • Created a repository of over 550 proteins with precomputed fragment maps, druggable hot spots, and water maps.
  • Enabled users to upload their own protein structures or utilize those from the Protein Data Bank and AlphaFold DB.
  • Implemented algorithms to search large datasets for fragments in optimal orientations, ranked by binding-free energy.

Main Results:

  • BMaps offers access to a large, precomputed dataset for fragment-based drug design.
  • The application simplifies the identification and selection of fragments for improving drug affinity and properties.
  • BMaps integrates docking and energy minimization with FBDD in an automated, accessible web interface.

Conclusions:

  • BMaps significantly lowers the barrier to entry for fragment-based drug design.
  • The web application empowers a wider research community to utilize FBDD for drug discovery.
  • BMaps represents a unique, automated, and user-friendly platform for advancing FBDD.