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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 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,...
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...
Induced-fit Model01:13

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...

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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

Predicting enzymatic function from global binding site descriptors.

Andrea Volkamer1, Daniel Kuhn, Friedrich Rippmann

  • 1University of Hamburg, Center for Bioinformatics, Bundesstr 43, 20146 Hamburg, Germany.

Proteins
|November 15, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces DoGSiteScorer, a computational tool for protein functional annotation. It uses support vector machine (SVM) models to classify enzymes based on protein structure descriptors, achieving high prediction accuracy.

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

Background:

  • The increasing number of solved protein structures necessitates automated methods for functional annotation and classification.
  • Accurate protein function prediction is crucial for understanding biological processes and drug discovery.

Purpose of the Study:

  • To develop and validate a computational tool, DoGSiteScorer, for automatic protein functional annotation and classification.
  • To build and assess the performance of support vector machine (SVM) models for predicting enzyme function at different classification levels.

Main Methods:

  • DoGSiteScorer calculates global descriptors from protein 3D structures, focusing on predicted pockets.
  • Support vector machine (SVM) models were trained on descriptors from 26,632 enzyme pockets.
  • The models were evaluated using cross-validation across enzyme classes, subclasses, and substrate-specific sub-subclasses.

Main Results:

  • Achieved 68.2% accuracy in predicting the correct main enzyme class.
  • Demonstrated accuracies ranging from 62.8% to 80.9% for predicting enzyme subclasses.
  • Obtained a substrate-specific recall rate of 53.8% for a kinase subset.

Conclusions:

  • DoGSiteScorer effectively predicts protein function using structural descriptors and SVM models.
  • The method shows promise for annotating unknown proteins and advancing the field of protein function prediction.