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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...
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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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...
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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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Related Experiment Video

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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

Combining specificity determining and conserved residues improves functional site prediction.

Olga V Kalinina1, Mikhail S Gelfand, Robert B Russell

  • 1EMBL Heidelberg, Heidelberg, Germany. kalinina@embl.de

BMC Bioinformatics
|June 11, 2009
PubMed
Summary

This study introduces Specificity-Determining Positions (SDPs) to improve functional site prediction in proteins. By identifying residues crucial for ligand specificity, this method enhances accuracy for proteins with known structures but unclear functions.

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

Published on: July 14, 2015

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein function prediction

Background:

  • Predicting functionally important sites in proteins is challenging.
  • Current methods often rely on general sequence conservation, failing to distinguish between structural and functional residues or specific sub-functions.
  • Many protein families interact with diverse ligands, complicating the identification of residues critical for specific interactions.

Purpose of the Study:

  • To develop a novel method for predicting protein functional sites by identifying conserved positions and those determining ligand specificity.
  • To define and utilize Specificity-Determining Positions (SDPs) for improved functional site prediction.

Main Methods:

  • Identification of conserved positions within protein families.
  • Definition of Specificity-Determining Positions (SDPs) as residues conserved in sub-groups with common specificity but differing between groups.
  • Benchmarking the SDPsite approach on enzyme families with known 3D structures and bound substrates.

Main Results:

  • The SDPsite method accurately predicts residues in contact with bound substrates.
  • Incorporating SDPs significantly enhances the accuracy of functional site prediction.
  • The approach was successfully applied to diverse protein families with known structures but limited functional annotations.

Conclusions:

  • The SDPsite method offers a superior approach for predicting functional details in proteins.
  • This method aids in understanding the function of numerous protein structures lacking clear annotations.