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

5.3K
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...
5.3K
Conserved Binding Sites01:49

Conserved Binding Sites

2.0K
2.0K
Ligand Binding Sites02:40

Ligand Binding Sites

15.6K
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...
15.6K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.9K
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...
14.9K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

15.5K
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:
15.5K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.8K
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...
5.8K

You might also read

Related Articles

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

Sort by
Same author

SIRT3 activation by oroxylin A phosphate diethyl ester triggers mitochondrial dysfunction and apoptosis in non-small cell lung cancer.

International journal of biological sciences·2026
Same author

Point-of-care ultrasound training using near-peer training and remote Supervision: A pilot randomized controlled trial.

The ultrasound journal·2026
Same author

Ten Questions on Using Lung Ultrasonography to Diagnose and Manage Pneumonia in Hospital-at-Home Model: Part III-Synchronicity and Foresight.

Diagnostics (Basel, Switzerland)·2026
Same author

Lipid-like Carbon-Dot Liposomes for Enhanced Drug Delivery and Membrane Fluidity Modulation in the Treatment of Metastatic Triple-Negative Breast Cancer.

Small (Weinheim an der Bergstrasse, Germany)·2025
Same author

Ten Questions on Using Lung Ultrasonography to Diagnose and Manage Pneumonia in the Hospital-at-Home Model: Part I-Techniques and Patterns.

Diagnostics (Basel, Switzerland)·2025
Same author

Discovery of Potent Dengue Virus NS2B-NS3 Protease Inhibitors Among Glycyrrhizic Acid Conjugates with Amino Acids and Dipeptides Esters.

Viruses·2025

Related Experiment Video

Updated: Mar 10, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.7K

MIB: Metal Ion-Binding Site Prediction and Docking Server.

Yu-Feng Lin1, Chih-Wen Cheng1, Chung-Shiuan Shih1

  • 1Institute of Bioinformatics and Systems Biology, National Chiao Tung University , Hsinchu, 30050 Taiwan.

Journal of Chemical Information and Modeling
|December 16, 2016
PubMed
Summary

This study introduces MIB, a web server that predicts metal ion-binding residues in proteins. MIB aids in understanding protein function and interactions by identifying key binding sites and generating 3D structures.

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.2K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

70.0K

Related Experiment Videos

Last Updated: Mar 10, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.7K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.2K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

70.0K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein structure dictates biological function and interactions.
  • Metal ions are crucial components in approximately one-third of known protein structures.
  • Experimental identification of metal ion-binding sites is resource-intensive.

Purpose of the Study:

  • To develop a computational tool for predicting metal ion-binding residues in proteins.
  • To generate 3D structural models of proteins with predicted metal ion-bound sites.
  • To provide a web server for accessible prediction and docking of metal ions.

Main Methods:

  • Construction of binding templates for 12 types of metal ions based on conserved residue and structural proximity (within 3.5 Å).
  • Utilized the fragment transformation method for structural comparison, avoiding data training.
  • Employed adjusted scoring functions based on structural and residue similarity.

Main Results:

  • Successfully predicted metal ion-binding residues for 12 different metal ions.
  • Generated predicted 3D structures of metal ion-bound proteins.
  • Developed the MIB web server (http://bioinfo.cmu.edu.tw/MIB/) for public use.

Conclusions:

  • The MIB server offers an efficient, non-experimental method for identifying and characterizing metal ion-binding sites in proteins.
  • This tool facilitates the study of protein function, interactions, and the role of metal ions in biological systems.
  • MIB enhances structural biology and bioinformatics research by providing predictive capabilities for metal ion coordination.