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Related Concept Videos

Protein Organization01:24

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 Organization01:24

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 Organization01:13

Protein Organization

Overview
Protein Organization01:13

Protein Organization

Overview
Protein and Protein Structure02:15

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 can...
Protein and Protein Structures02:15

Protein and Protein Structures

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 can...

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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

ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses.

Jonathan Binkley1, Kalpana Karra, Andrew Kirby

  • 1Stanford University School of Medicine, Departments of Pathology and Genetics, Stanford, California 94305, USA.

Genome Research
|October 23, 2009
PubMed
Summary

ProPhylER predicts eukaryotic protein evolution and mutation impact using comparative sequence analysis. This resource aids structure-function studies and polymorphism prediction with high accuracy.

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Last Updated: Jun 19, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Published on: July 8, 2025

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Comparative sequence analysis is crucial for understanding protein evolution.
  • Predicting mutation impact and evolutionary constraint informs protein function and structure research.

Purpose of the Study:

  • To introduce ProPhylER, a curated proteome resource for analyzing protein evolution.
  • To provide tools for predicting evolutionary constraint and mutation impact in eukaryotic proteins.

Main Methods:

  • Utilized comparative sequence analysis on nearly 9000 protein clusters (>200,000 sequences).
  • Developed two interfaces: ProPhylER Interface (sequence space analysis) and CrystalPainter (structure mapping).
  • Evaluated a unique regional analysis of evolutionary constraint.

Main Results:

  • ProPhylER offers predictive analyses of evolutionary constraint and mutation impact.
  • The resource effectively maps evolutionary constraints onto protein structures.
  • Regional analysis demonstrates high accuracy, complementing single-site analysis.

Conclusions:

  • ProPhylER enhances structure-function investigations through accurate evolutionary constraint analysis.
  • The resource aids in predicting the impact of protein polymorphisms.
  • ProPhylER serves as a valuable tool for diverse research programs involving protein analysis.