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Conservation of Protein Domains Over Different Proteins

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...

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...

Conservation of Protein Domains

Conservation of Protein Domains

Protein and Protein Structures

Protein and Protein Structures

Conserved Binding Sites

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...

Conserved Binding Sites

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Comparing co-evolution methods and their application to template-free protein structure prediction.

Saulo Henrique Pires de Oliveira¹, Jiye Shi^2,3, Charlotte M Deane¹

¹Department of Statistics, University of Oxford, Oxford OX1 3LB, UK.

Bioinformatics (Oxford, England)

|February 8, 2017

Summary

Co-evolution methods predict protein residue contacts, but their utility for protein model generation varies. MetaPSICOV stage 1 predictions, not the most precise, yielded superior models and improved decoy selection.

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

Computational Biology
Structural Bioinformatics
Protein Modeling

Background:

Co-evolution methods predict residue contacts, crucial for understanding protein structure.
Previous comparisons focused on prediction precision, neglecting utility in de novo model generation.

Purpose of the Study:

To compare the effectiveness of different co-evolution methods for protein model generation.
To assess the correlation between predicted contacts and model quality.

Main Methods:

Eight co-evolution methods were evaluated on ~3500 proteins.
Contact predictions were used to assist de novo protein model generation.
A novel method for classifying correct/incorrect models based on satisfied long-range contacts was developed.

Main Results:

MetaPSICOV stage 2 offered the highest average prediction precision, but stage 1 predictions generated better models.
Model quality correlated with the proportion of satisfied long-range predicted contacts.
Classifying models using this proportion enriched good decoys by sevenfold and retained 17/18 correct models.

Conclusions:

The choice of co-evolution method impacts protein model generation quality.
A new metric effectively filters incorrect protein models, enhancing the reliability of structural modeling ensembles.