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Related Concept Videos

Protein Organization01:24

Protein Organization

8.8K
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....
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Protein Organization01:13

Protein Organization

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Overview
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Protein and Protein Structures02:15

Protein and Protein Structures

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Protein and Protein Structure02:15

Protein and Protein Structure

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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...
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Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
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Protein Families02:47

Protein Families

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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...
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Updated: Dec 29, 2025

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

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Comparative Protein Structure Analysis with Bio3D-Web.

Barry J Grant1, Lars Skjærven2, Xin-Qiu Yao3

  • 1Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA. bjgrant@ucsd.edu.

Methods in Molecular Biology (Clifton, N.J.)
|February 2, 2020
PubMed
Summary
This summary is machine-generated.

Bio3D-web offers an interactive online platform for analyzing protein sequence-structure-dynamics. This tool aids researchers in characterizing homologous proteins by assessing structural and dynamic properties, facilitating biological insights.

Keywords:
Protein dynamicsProtein flexibilityProtein structureSequence-structure-function relationshipsStructural bioinformatics

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Biophysics

Background:

  • Understanding protein structure-dynamics relationships is crucial for molecular biology.
  • Analyzing homologous proteins requires integrated tools for sequence, structure, and dynamics.

Purpose of the Study:

  • To present Bio3D-web, an online application for interactive analysis of protein sequence-structure-dynamics.
  • To provide a comprehensive platform for characterizing homologous proteins using available structural data.

Main Methods:

  • Interactive analysis of user-defined protein structure sets.
  • Structure database searching, sequence and structure conservation assessment.
  • Principal Component Analysis (PCA) for clustering and inter-conformer mapping.
  • Ensemble Normal Mode Analysis (eNMA) for flexibility prediction.

Main Results:

  • Bio3D-web enables comprehensive characterization of structural, conformational, and dynamic properties of homologous proteins.
  • The application integrates various computational methods for in-depth protein analysis.
  • Customizable reports (PDF, Word, HTML) detailing analysis settings and results are generated.

Conclusions:

  • Bio3D-web provides a powerful, accessible resource for researchers studying protein structure-dynamics.
  • The platform facilitates the exploration of homologous protein families from sequence or structure data.
  • Availability as a web application, Docker image, and source code enhances accessibility.