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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,...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Protein-protein Interfaces02:04

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 polypeptide...
Protein-Protein Interfaces02:04

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 polypeptide...

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Related Experiment Video

Updated: Jun 13, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

BioPhysConnectoR: Connecting sequence information and biophysical models.

Franziska Hoffgaard1, Philipp Weil, Kay Hamacher

  • 1Theoretical Biology and Bioinformatics, Institute of Microbiology and Genetics, Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64289 Darmstadt, Germany. hoffgaard@bio.tu-darmstadt.de

BMC Bioinformatics
|April 24, 2010
PubMed
Summary
This summary is machine-generated.

Understanding protein coevolution is challenging. BioPhysConnectoR, an R package, links sequence data to biophysical properties, enabling functional annotation of evolutionary changes.

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Last Updated: Jun 13, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
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Published on: July 12, 2022

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09:51

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

Published on: July 16, 2017

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:

  • Computational Biology
  • Biophysics
  • Bioinformatics

Background:

  • Understanding coevolution in biomolecular systems, particularly proteins, remains a significant challenge.
  • Current sequence-based methods identify coevolving residues but lack biophysical context.
  • Detailed atomistic simulations are computationally expensive, limiting their application.

Purpose of the Study:

  • To develop a framework connecting sequence-based coevolutionary information with biophysical properties.
  • To enable functional annotation of evolutionary sequence changes using reduced molecular models.
  • To provide an efficient computational tool for biomolecular design and evolutionary studies.

Main Methods:

  • Development of the R package BioPhysConnectoR.
  • Integration of information-theoretical methods with reduced molecular models.
  • Leveraging multi-core architectures for parallelized computations.

Main Results:

  • BioPhysConnectoR connects the information-theoretical domain of biomolecular sequences to biophysical properties.
  • The package integrates fragmented ideas into a single, usable framework for R.
  • Computational time for evolutionary and biomolecular design studies is reduced.

Conclusions:

  • BioPhysConnectoR is an R package facilitating functional annotation of sequence-level coevolution.
  • The package is distributed under GPL 2 license.
  • It enables efficient and parallelized annotation of coevolutionary data.