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Related Concept Videos

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,...
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,...
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 Organization01:24

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.
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Updated: May 11, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

MAP(2.0)3D: a sequence/structure based server for protein engineering.

Rajni Verma1, Ulrich Schwaneberg, Danilo Roccatano

  • 1School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.

ACS Synthetic Biology
|May 9, 2013
PubMed
Summary
This summary is machine-generated.

The Mutagenesis Assistant Program (MAP) 2.0 3D tool enhances protein engineering by analyzing mutational biases and correlating them with protein structures. This helps select optimal random mutagenesis methods for directed evolution experiments.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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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

Area of Science:

  • Protein Engineering
  • Bioinformatics
  • Computational Biology

Background:

  • Directed evolution experiments rely on random mutagenesis to generate protein variants.
  • Analyzing mutational biases is crucial for selecting effective mutagenesis methods.
  • Existing tools like MAP provide statistical analysis of amino acid substitutions.

Purpose of the Study:

  • To introduce an improved web-based tool, MAP(2.0)3D, for analyzing mutational biases in protein engineering.
  • To correlate amino acid substitution patterns with protein structural information.
  • To aid protein engineers in selecting suitable random mutagenesis strategies.

Main Methods:

  • Development of the MAP(2.0)3D server, an updated version of the Mutagenesis Assistant Program.
  • Integration of structural correlation features, including secondary and tertiary structure analysis.
  • Analysis of specific structural components: hydrogen bonds, hydrophobic contacts, salt bridges, solvent accessibility, and B-factors.

Main Results:

  • The MAP(2.0)3D server correlates mutational biases with protein structural features.
  • Novel indicators are represented on secondary and tertiary protein structures.
  • Demonstration of the server's capability using D-amino oxidase, phytase, and N-acetylneuraminic acid aldolase.

Conclusions:

  • MAP(2.0)3D provides enhanced insights into mutational biases by incorporating structural data.
  • The tool facilitates informed selection of random mutagenesis methods for protein engineering.
  • The server is publicly accessible, supporting advancements in directed evolution research.