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

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...
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 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...
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...
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...
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...

You might also read

Related Articles

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

Sort by
Same author

The social significance of golf in Finland in the year 2021 based on SROI analysis.

Frontiers in sports and active living·2026
Same author

Immediate and Mid-Long-Term Effects of Foot Orthoses on Gait Biomechanics and Clinical Characteristics in Medial Knee Osteoarthritis: A Systematic Review and Meta-analysis.

Annals of biomedical engineering·2026
Same author

Patient-Specific Determinants of Response to BCMA- and GPRC5D-Targeted CAR T-Cell Therapy in Multiple Myeloma: A QSP Analysis of Clinical Trial and Real-World Data.

Clinical pharmacology and therapeutics·2026
Same author

Advancing Conservative Treatment of Knee Osteoarthritis: 3D-Printed Shoe Soles for Passive Toe-Out Gait Modification.

Journal of foot and ankle research·2026
Same author

Pose-aware deep perceptual similarity for iterative 2D/3D registration of knee joints using contrastive learning.

International journal of computer assisted radiology and surgery·2026
Same author

Passive Laxity in Patients With Subjective Instability Following a Cruciate-Retaining Total Knee Arthroplasty: A Pilot Study.

JB & JS open access·2026

Related Experiment Video

Updated: Jul 7, 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

Functional site prediction selects correct protein models.

Vijayalakshmi Chelliah1, William R Taylor

  • 1Division of Mathematical Biology, The National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. vchelli@nimr.mrc.ac.uk

BMC Bioinformatics
|March 20, 2008
PubMed
Summary
This summary is machine-generated.

Predicting protein functional sites aids in identifying correct protein structures. A new scoring method effectively ranks models with clustered predicted functional residues, distinguishing native-like protein models from decoys.

More Related Videos

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

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: Jul 7, 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

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

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:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • Protein structure prediction is crucial for understanding protein function.
  • Knowledge of functional sites can guide protein structure modeling.
  • Predicting residues likely to be part of functional sites is possible even without prior functional information.

Purpose of the Study:

  • To develop a method for predicting protein functional sites.
  • To utilize predicted functional site information for selecting accurate protein models.
  • To enhance the discrimination between native and non-native protein models.

Main Methods:

  • Devised a scoring method using a large dataset of protein-like decoy models.
  • Focused on clustering of predicted functional site residues.
  • Tested the method on various small and large alpha/beta/alpha proteins (enzymes and non-enzymes).

Main Results:

  • The devised score successfully ranked models with clustered predicted functional residues highly.
  • Models corresponding to the native fold were consistently ranked at the top.
  • The method demonstrated robust performance on proteins not involved in its development.

Conclusions:

  • Predicted functional site positions serve as an effective filter for distinguishing native-like protein models.
  • This method is applicable to any set of protein models.
  • It offers a valuable tool to complement various protein modeling approaches, including ab initio and homology-based methods.