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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 Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: Jun 10, 2026

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

Effective 3D protein structure prediction with local adjustment genetic-annealing algorithm.

Xiao-Long Zhang1, Xiao-Li Lin

  • 1School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, 430081, China. xiaolong.zhang@wust.edu.cn

Interdisciplinary Sciences, Computational Life Sciences
|July 27, 2010
PubMed
Summary

Predicting protein tertiary structure is complex. The local adjustment genetic-annealing (LAGA) algorithm improves accuracy for the 3D off-lattice AB model, outperforming previous methods in protein folding studies.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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10:58

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

Published on: July 25, 2013

Area of Science:

  • Computational biology
  • Biophysics
  • Bioinformatics

Background:

  • The protein folding problem involves predicting a protein's 3D structure from its amino acid sequence.
  • This prediction is computationally intensive and considered NP-hard for certain models like the 3D off-lattice AB model.
  • Accurate protein structure prediction is crucial for understanding protein function and disease.

Purpose of the Study:

  • To develop and evaluate a novel algorithm for protein structure prediction.
  • To address the computational challenges of the protein folding problem using the 3D off-lattice AB model.
  • To improve the accuracy and performance of protein structure prediction methods.

Main Methods:

  • The study employed the local adjustment genetic-annealing (LAGA) algorithm.
  • LAGA incorporates improved crossover and mutation strategies.
  • A local adjustment strategy was integrated to enhance the search capabilities for the protein's ground state.

Main Results:

  • Experiments were conducted using Fibonacci sequences on the 3D off-lattice AB model.
  • The LAGA algorithm demonstrated superior performance compared to existing methods.
  • Enhanced accuracy in predicting protein folding structures was observed.

Conclusions:

  • The LAGA algorithm is an effective approach for solving the protein folding problem.
  • The developed algorithm offers improved accuracy and efficiency for protein structure prediction.
  • LAGA shows promise for advancing computational approaches in structural biology.