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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...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
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...
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,...
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...
Protein Folding01:22

Protein Folding

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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

Prediction of protein functional residues from sequence by probability density estimation.

J D Fischer1, C E Mayer, J Söding

  • 1Department for Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany.

Bioinformatics (Oxford, England)
|January 5, 2008
PubMed
Summary

Predicting protein functional sites is crucial for research. Our new method, FRcons, improves prediction accuracy for ligand-binding and catalytic residues using evolutionary conservation and structural features.

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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:

  • Protein bioinformatics
  • Computational biology
  • Structural bioinformatics

Background:

  • Predicting ligand-binding and catalytic residues aids genetic and biochemical studies.
  • Existing sequence-based methods suffer from low precision in identifying these functional residues.
  • Current methods rely heavily on evolutionary conservation from multiple sequence alignments.

Purpose of the Study:

  • To develop a more precise method for predicting protein functional residues.
  • To enhance the accuracy of identifying ligand-binding and catalytic sites.
  • To overcome limitations of existing sequence-based prediction techniques.

Main Methods:

  • Combined evolutionary conservation, amino acid distribution, predicted secondary structure (ss), and relative solvent accessibility (rsa).
  • Measured conservation by comparing site amino acid distribution to expected distributions for predicted ss and rsa states.
  • Incorporated neighboring residue conservation and used conditional probability density estimation for functional site probability.

Main Results:

  • The FRcons method demonstrates higher precision in predicting both ligand-binding and catalytic residues compared to existing methods.
  • Achieved 50% precision for ligand-binding residues and 40% precision for catalytic residues at 20% sensitivity.
  • Validated performance using large datasets from the Catalytic Site Atlas and PDB SITE records.

Conclusions:

  • FRcons offers a significant improvement in predicting protein functional residues.
  • The integration of diverse features enhances prediction accuracy.
  • This method provides a valuable tool for guiding protein research.