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Protein Families

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...

Protein Families

Protein Families

Protein-protein Interfaces

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...

Protein-Protein Interfaces

Protein-Protein Interfaces

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...

Structural Protein Function

Structural Protein Function

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Related Experiment Video

Updated: Apr 17, 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

Template-based prediction of protein function.

Donald Petrey¹, T Scott Chen¹, Lei Deng¹

¹Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Department of Systems Biology, Center for Computational Biology and Bioinformatics, 1130 St. Nicholas Avenue, Room 815, New York, NY 10032, United States.

Current Opinion in Structural Biology

|February 14, 2015

Summary

This summary is machine-generated.

Structure-based protein function annotation uses known protein structures to predict the function of new proteins. Recent advances enable proteome-wide analysis, expanding beyond traditional sequence comparison methods.

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Area of Science:

Biochemistry
Structural Biology
Bioinformatics

Background:

Protein function annotation is crucial for understanding biological systems.
Template-based methods infer function from known structures and functions.
Traditional methods rely heavily on sequence similarity.

Purpose of the Study:

To review recent advances in structure-based protein function annotation.
To highlight template-based methods and template identification strategies.
To discuss the expanding applicability of structural information in function prediction.

Main Methods:

Focus on template-based approaches for protein function annotation.
Discuss template identification via sequence analysis.
Introduce structure-based similarity methods for template identification.
Leverage homology modeling and structural information.

Main Results:

Structure-based methods now complement and expand upon sequence-based approaches.
New methods identify functional relationships missed by sequence analysis.
Proteome-wide application of template-based methods is increasingly feasible.
Structural information significantly broadens function annotation capabilities.

Conclusions:

Structure-based protein function annotation is rapidly advancing.
Template-based methods, especially those using structural similarity, are powerful tools.
These advancements enhance our ability to annotate protein functions across entire proteomes.