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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

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

Protein-protein Interfaces

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...

Protein-Protein Interfaces

Protein-Protein Interfaces

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Related Experiment Video

Updated: May 2, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

iview: an interactive WebGL visualizer for protein-ligand complex.

Hongjian Li¹, Kwong-Sak Leung, Takanori Nakane

¹Department of Computer Science and Engineering, Chinese University of Hong Kong, Hong Kong, China. jackyleehongjian@gmail.com.

BMC Bioinformatics

|February 26, 2014

Summary

This summary is machine-generated.

We developed iview, an interactive WebGL visualizer for protein-ligand complexes, enhancing drug design. This tool offers virtual reality support and advanced surface representations for better interaction identification.

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Area of Science:

Computational chemistry
Structural biology
Drug discovery

Background:

Protein-ligand complex visualization is crucial for understanding interactions and designing drugs.
Existing web visualizers often suffer from slow rendering or lack virtual reality (VR) capabilities.
Macromolecular surface construction is a missing feature in many current tools.

Purpose of the Study:

To develop an easy-to-use, interactive WebGL-based visualizer for protein-ligand complexes.
To incorporate hardware acceleration for faster rendering compared to software-based methods.
To provide virtual reality support and advanced surface representations for enhanced visualization.

Main Methods:

Developed iview, an interactive WebGL visualizer utilizing hardware acceleration.
Implemented VR features including anaglyph, parallax barrier, and Oculus Rift support.
Integrated four types of surface representations: Van der Waals, solvent excluded, solvent accessible, and molecular surfaces.

Main Results:

iview provides visually appealing identification of intermolecular interactions through VR.
Supports multiple surface representations for comprehensive analysis.
A specialized version of iview was created for the istar web platform, demonstrating its portability for protein-ligand docking.

Conclusions:

iview offers a user-friendly, platform-independent visualizer leveraging innovative 3D techniques.
It enhances accessibility for researchers without aiming to replace professional visualization software.
The tool facilitates easier exploration of protein-ligand interactions and aids in drug design.