Related Experiment Video
Updated: Mar 10, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
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.
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.
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.
Related Concept Videos
Conserved Binding Sites
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...
Conserved Binding Sites
Ligand Binding Sites
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...
Protein-protein Interfaces
The Equilibrium Binding Constant and Binding Strength
Ligand Binding and Linkage

