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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 Organization01:13

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.
Protein Families02:47

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 locations, protein...
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...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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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

deconSTRUCT: general purpose protein database search on the substructure level.

Zong Hong Zhang1, Kavitha Bharatham, Westley A Sherman

  • 1Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore.

Nucleic Acids Research
|June 5, 2010
PubMed
Summary
This summary is machine-generated.

DeconSTRUCT is a fast web server for detecting similar protein substructures by analyzing secondary structure elements (SSEs). It offers sensitive and specific protein structure comparisons with rapid results.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biochemistry

Background:

  • Protein structure comparison is crucial for understanding protein function and evolution.
  • Existing methods for protein substructure detection can be computationally intensive.
  • Efficient algorithms are needed to accelerate the analysis of large protein databases.

Purpose of the Study:

  • To introduce deconSTRUCT, a novel web server for general-purpose protein substructure detection.
  • To provide a sensitive and specific method for identifying similar protein (sub)structures.
  • To achieve significantly increased search speeds compared to established methods.

Main Methods:

  • Deconstruction of query protein structures into secondary structure elements (SSEs).
  • Reassembly of SSEs based on similarity in direction and sequential order.
  • Hierarchical organization of protein structure information for efficient searching.
  • Post-processing to construct backbone atom-level matches.

Main Results:

  • DeconSTRUCT achieves high sensitivity and specificity in detecting similar protein substructures.
  • The server demonstrates orders of magnitude increase in speed compared to existing search engines.
  • Results include matched SSEs, transformation matrices for superposition, and visualization tools.

Conclusions:

  • DeconSTRUCT provides a fast and effective tool for protein substructure similarity detection.
  • The method's efficiency allows for rapid analysis of large structural datasets.
  • The web server offers a valuable resource for researchers in structural biology and bioinformatics.