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

4.4K
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...
4.4K
Proteomics01:33

Proteomics

8.0K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
8.0K
Protein-protein Interfaces02:04

Protein-protein Interfaces

13.8K
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...
13.8K
Ligand Binding Sites02:40

Ligand Binding Sites

13.6K
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...
13.6K

You might also read

Related Articles

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

Sort by
Same author

Whole metagenome sequencing: not deep enough for complete microbial function recovery.

Microbiome·2026
Same author

Mars sample return campaign: biological risk and a proposed sample safety assessment protocol.

Applied and environmental microbiology·2026
Same author

16S rRNA sequence captures microbial functional potential.

bioRxiv : the preprint server for biology·2026
Same author

Quantifying uncertainty in protein representations across models and tasks.

Nature methods·2026
Same author

Whole Metagenome Sequencing: not Deep Enough for Complete Microbial Function Recovery.

bioRxiv : the preprint server for biology·2025
Same author

The CoREST Complex Regulates Alternative Splicing by the Transcriptional Regulation of RNA Processing Genes in Melanoma Cells.

Cells·2025
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Sep 21, 2025

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

2.0K

mebipred: identifying metal-binding potential in protein sequence.

A A Aptekmann1,2, J Buongiorno3, D Giovannelli2,4,5

  • 1Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA.

Bioinformatics (Oxford, England)
|May 31, 2022
PubMed
Summary
This summary is machine-generated.

A new machine learning tool, Mebipred, accurately identifies metal-binding proteins from sequence data. This method aids in understanding cellular activity and microbiome metal requirements, offering a faster and more precise alternative to existing techniques.

More Related Videos

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides
11:04

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Published on: September 7, 2019

9.3K
Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

9.7K

Related Experiment Videos

Last Updated: Sep 21, 2025

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

2.0K
Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides
11:04

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Published on: September 7, 2019

9.3K
Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

9.7K

Area of Science:

  • Biochemistry and Molecular Biology
  • Bioinformatics and Computational Biology
  • Microbiology

Background:

  • Metal-binding proteins are essential for numerous biological processes, including catalysis and structural stability.
  • Identifying these proteins is crucial for understanding cellular mechanisms, yet experimental annotation is limited.
  • Current computational methods for predicting metal-binding proteins are often imprecise and have restricted applications.

Purpose of the Study:

  • To develop a novel, accurate, and efficient computational method for identifying metal-binding proteins from sequence data.
  • To enable the annotation of specific metal ions bound by proteins.
  • To explore the utility of this method in analyzing metal requirements in various microbiomes.

Main Methods:

  • Developed Mebipred, a machine learning-based method utilizing sequence-derived features.
  • The method is reference-free, avoiding computationally intensive sequence alignments.
  • Evaluated Mebipred's accuracy and applicability on short sequence stretches and microbiome data.

Main Results:

  • Mebipred achieves over 80% accuracy in identifying proteins that bind metal ion-containing ligands.
  • The method can annotate the specific identity of 11 common metal ions.
  • Mebipred is faster and more accurate than existing sequence-based prediction methods.
  • Analysis of microbiome data revealed diverse metal usage across different environments, with human microbiomes showing distinct preferences influenced by physiological conditions.

Conclusions:

  • Mebipred provides a highly accurate and efficient tool for identifying metal-binding proteins.
  • The method is valuable for analyzing metal requirements in metagenomic samples and understanding microbial ecology.
  • Mebipred advances the computational prediction of protein function and metal ion interactions.