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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 Organization01:13

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 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

Efficient approaches for retrieving protein tertiary structures.

Georgina Mirceva1, Ivana Cingovska, Zoran Dimov

  • 1Department of Computer Science and Computer Engineering, Faculty of Electrical Engineering and Information Technologies, Ss. Cyril and Methodius University in Skopje, PO Box 574, 1000 Skopje, Macedonia. georgina@feit.ukim.edu.mk

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|October 26, 2011
PubMed
Summary

This study introduces novel computational methods for fast and accurate protein structure retrieval. New descriptors and an efficient alignment algorithm (MASASW) improve speed and accuracy, aiding drug development.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Drug Discovery

Background:

  • Protein 3D conformation dictates function, crucial for understanding biological processes.
  • Rapid discovery of new proteins necessitates efficient computational methods for structure retrieval.
  • Accurate protein structure-function relationship analysis is vital for novel drug development.

Purpose of the Study:

  • To present novel computational approaches for retrieving protein tertiary structures.
  • To develop fast and accurate algorithms for protein structure analysis.
  • To enhance the understanding of structure-function relationships for drug discovery.

Main Methods:

  • Development of voxel-based and ray-based protein descriptors.
  • Introduction of five novel wavelet descriptors utilizing protein distance matrices.
  • Proposal of an efficient distance matrix alignment algorithm: Matrix Alignment by Sequence Alignment within Sliding Window (MASASW).

Main Results:

  • Novel descriptors (ray, wavelet) and MASASW demonstrate high accuracy in protein structure retrieval.
  • MASASW algorithm significantly outperforms existing methods like DALI, CE, and MatAlign in speed and accuracy.
  • Proposed methods are generally fast and accurate compared to existing algorithms.

Conclusions:

  • The developed voxel-based, ray-based, and wavelet-based descriptors offer efficient protein structure retrieval.
  • MASASW provides a highly accurate and efficient solution for distance matrix alignment.
  • These advancements accelerate the analysis of protein structures, supporting drug development.