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

Ligand Binding Sites02:40

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...
Protein-protein Interfaces02:04

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 polypeptide...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Ligand Binding and Linkage00:49

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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...

You might also read

Related Articles

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

Sort by
Same author

[Platelet parameters and platelet Toll-like receptor 4 (TLR4) expression in patients with sepsis, and the effect of a joint treatment-plan integrating traditional Chinese and western medicine: a clinical study].

Zhongguo wei zhong bing ji jiu yi xue = Chinese critical care medicine = Zhongguo weizhongbing jijiuyixue·2011
Same author

A novel kernel Fisher discriminant analysis: constructing informative kernel by decision tree ensemble for metabolomics data analysis.

Analytica chimica acta·2011
Same author

Anterior debridement and reconstruction via thoracoscopy-assisted mini-open approach for the treatment of thoracic spinal tuberculosis: minimum 5-year follow-up.

European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society·2011
Same author

[A family-based association study of FXYD6 gene polymorphisms and schizophrenia].

Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics·2011
Same author

Prenatal diagnosis of penoscrotal transposition with 2- and 3-dimensional ultrasonography.

Journal of ultrasound in medicine : official journal of the American Institute of Ultrasound in Medicine·2011
Same author

Differentiation of α- or β-aspartic isomers in the heptapeptides by the fragments of [M + Na]+ using ion trap tandem mass spectrometry.

Journal of the American Society for Mass Spectrometry·2011

Related Experiment Video

Updated: Jun 9, 2026

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

Protein binding hot spots prediction from sequence only by a new ensemble learning method.

Shan-Shan Hu1,2, Peng Chen3,4,5, Bing Wang6

  • 1School of Computer Science and Technology, Anhui University, Hefei, 230601, Anhui, China.

Amino Acids
|August 3, 2017
PubMed
Summary

This study introduces a novel computational method for predicting protein binding hot spots using only amino acid sequences. The new model significantly improves hot spot identification accuracy, aiding drug design.

Keywords:
Ensemble systemHot spot residueIBk

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Related Experiment Videos

Last Updated: Jun 9, 2026

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

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Biochemistry
  • Computational Biology
  • Bioinformatics

Background:

  • Hot spots are crucial protein binding regions targeted in drug design.
  • Experimental hot spot identification is time-consuming and expensive.
  • Sequence-based prediction is valuable due to limitations in protein structure availability.

Purpose of the Study:

  • To develop a novel, sequence-based computational model for predicting protein hot spots.
  • To enhance the efficiency and accuracy of hot spot identification for drug discovery applications.

Main Methods:

  • A sequence-based model combining physicochemical features and relative accessible surface area was developed.
  • The model utilizes 83 Instance-based k-means (IBk) classifiers trained on properties from the AAindex1 database.
  • An ensemble classifier was created using a majority voting technique from top-performing classifiers.

Main Results:

  • The proposed ensemble classifier achieved an F1 score of 0.80 on the binding interface database (BID) test set.
  • The model demonstrated superior performance compared to existing state-of-the-art computational methods.
  • The sequence-based approach proved effective for hot spot prediction.

Conclusions:

  • The developed sequence-based model offers a more practical and efficient approach to hot spot prediction.
  • This method can accelerate drug design by accurately identifying critical binding regions.
  • The findings highlight the potential of integrating physicochemical properties and surface area information for protein-protein interaction site prediction.