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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 analyses the...

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 analyses the...

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 form...

Conservation of Protein Domains

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...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

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Related Experiment Video

Updated: Jun 13, 2026

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

Quality assessment of protein model-structures using evolutionary conservation.

Matan Kalman¹, Nir Ben-Tal

¹Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.

Bioinformatics (Oxford, England)

|April 14, 2010

Summary

ConQuass is a new protein structure quality assessment tool. It uses residue conservation patterns to identify flawed models, showing performance comparable to existing methods.

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Last Updated: Jun 13, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

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

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 modeling

Background:

Protein structural model quality assessment is crucial for validating structure determination and guiding model building.
Existing methods often rely on properties of native structures, which may not apply to flawed models.
The distribution of conserved residues in the core and variable residues at the surface of native proteins is an underutilized property for quality assessment.

Purpose of the Study:

To introduce ConQuass, a novel computational tool for assessing protein structural model quality.
To evaluate ConQuass's ability to identify problematic models using protein conservation patterns.
To compare ConQuass's performance against existing methods in a benchmark dataset.

Main Methods:

Developed ConQuass, a quality assessment program integrating protein structure and conservation patterns.
Utilized residue conservation data to evaluate the consistency of structural models.
Assessed model quality scores against known native structures in the CASP8 dataset.

Main Results:

ConQuass successfully identifies problematic protein structural models.
Scores generated by ConQuass for CASP8 server models correlate with their similarity to native structures.
When conservation data is reliable, ConQuass demonstrates comparable and complementary performance to other single-structure assessment methods not using homologous information.

Conclusions:

ConQuass offers a novel approach to protein structure quality assessment by leveraging conservation patterns.
The tool is effective in distinguishing between accurate and inaccurate structural models.
ConQuass provides a valuable and complementary method to existing quality assessment strategies, especially when homologous structural information is limited.