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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...
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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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,...

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Related Experiment Video

Updated: Jul 13, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Bayesian refinement of protein functional site matching.

Kanti V Mardia1, Vysaul B Nyirongo, Peter J Green

  • 1Department of Statistics, University of Leeds, Leeds, UK. k.v.mardia@leeds.ac.uk <k.v.mardia@leeds.ac.uk>

BMC Bioinformatics
|July 21, 2007
PubMed
Summary

A new Bayesian approach refines protein functional site matching using Markov chain Monte Carlo (MCMC). This method improves accuracy and identifies more significant matches than traditional graph-based techniques.

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Last Updated: Jul 13, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • Matching protein functional sites is crucial for understanding protein function and evolution.
  • Existing graph-based methods struggle with distance threshold adjustments and identifying alternative solutions.
  • Bayesian approaches offer flexibility in incorporating prior information, unlike combinatorial methods.

Purpose of the Study:

  • To develop a novel meta-algorithm for matching protein functional sites.
  • To improve upon existing graph-based methods by incorporating a Bayesian approach.
  • To account for both 3D structure and physico-chemical properties of amino acids.

Main Methods:

  • A meta-algorithm combining initial graph matching with Markov chain Monte Carlo (MCMC) refinement.
  • The MCMC procedure accounts for 3D site structure and amino acid physico-chemical properties.
  • Application to matching NAD(P)(H) binding sites across various protein families and folds.

Main Results:

  • The MCMC refinement significantly enhances graph-based protein site matches.
  • The method increases the number of significant matches compared to traditional graph methods, validated by p-values.
  • Significant matches were found between binding sites for the same cofactor across different protein families and folds.

Conclusions:

  • The MCMC refinement step substantially improves graph-based functional site matching.
  • The study highlights cases where shape-based matches lack similar amino acid chemistry, even within families.
  • The procedure successfully identifies significant matches for cofactor binding sites across diverse protein structures.