Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Ligand Binding Sites

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 Sites

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 Linkage

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...

Ligand Binding and Linkage

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...

You might also read

Related Articles

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

Sort by

Same author

Bone marrow immunosuppressive states associate with survival after guadecitabine and atezolizumab therapy in HMA-R/R MDS.

Blood neoplasia·2026

Same author

Bone marrow microenvironment signatures associate with patient survival after guadecitabine and atezolizumab therapy in HMA-resistant MDS.

bioRxiv : the preprint server for biology·2024

Same author

Genetic diversity in the IZUMO1-JUNO protein-receptor pair involved in human reproduction.

PloS one·2021

Same author

Erratum to: Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology.

BMC genomics·2016

Same author

Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology.

BMC genomics·2016

Same author

A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4.

The Journal of chemical physics·2016

Search research articles

Related Experiment Video

Updated: Jun 26, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

A cluster-aware graphical user interface for a virtual ligand screening tool.

Zachary H Ramjan¹, Amar Raheja, Wely B Floriano

¹Bioinformatics and Computational Biology group at the California State Polytechnic University, Pomona 91768, USA. zhramjan@csupomona.edu

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

|January 24, 2009

Summary

A new Graphical User Interface (GUI) enhances Cassandra, a Virtual Ligand Screening (VLS) application. This GUI simplifies complex data management and analysis, improving efficiency and user accessibility for VLS projects.

More Related Videos

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Related Experiment Videos

Last Updated: Jun 26, 2026

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Area of Science:

Computational Chemistry
Bioinformatics
Software Engineering

Background:

Virtual Ligand Screening (VLS) is crucial for drug discovery.
Existing VLS applications like Cassandra can have a steep learning curve.
Efficient data management and user-friendliness are key to maximizing VLS utility.

Purpose of the Study:

To design and implement a user-friendly Graphical User Interface (GUI) for the Cassandra VLS application.
To improve the accessibility and efficiency of executing VLS projects.
To facilitate management of concurrent data paths on single machines and High Performance Computing Clusters (HPCC).

Main Methods:

The GUI was developed using Trolltech QT4 and Perl.
The interface allows for management of multiple, concurrent, interactive data paths.
Implementation focused on simplifying user interaction and workflow.

Main Results:

The GUI significantly reduced the complexity and learning curve associated with Cassandra.
Average execution time for VLS projects was decreased.
User training time was reduced, leading to an increased user base.

Conclusions:

The developed GUI enhances the usability and efficiency of the Cassandra VLS application.
Optimized data handling and analysis contribute to faster drug discovery pipelines.
Increased user adoption and efficiency demonstrate the GUI's successful implementation.