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Related Concept Videos

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...
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-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...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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...
Protein Folding01:22

Protein Folding

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Updated: Jun 12, 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

3D protein structure prediction with genetic tabu search algorithm.

Xiaolong Zhang1, Ting Wang, Huiping Luo

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

BMC Systems Biology
|June 5, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a hybrid genetic algorithm (GA) and tabu search (TS) algorithm for protein structure prediction (PSP). The novel GATS algorithm improves efficiency and accuracy in predicting 3D protein structures.

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

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Last Updated: Jun 12, 2026

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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

Area of Science:

  • Computational biology
  • Bioinformatics
  • Biophysics

Background:

  • Protein structure prediction (PSP) is crucial for drug design and disease prediction.
  • The complexity of protein structures necessitates simplified models like the off-lattice AB model.
  • PSP is an NP-hard problem, requiring efficient optimization algorithms.

Purpose of the Study:

  • To develop an efficient hybrid algorithm for protein structure prediction.
  • To address the global optimization challenge in PSP using a combination of algorithms.

Main Methods:

  • A hybrid algorithm combining genetic algorithm (GA) and tabu search (TS) was developed.
  • Improved strategies include integrating TS into GA operators, variable population size, and ranking selection.
  • The algorithm, termed GATS, was tested on Fibonacci and real protein sequences.

Main Results:

  • The GATS algorithm demonstrated improved efficiency and local search capability.
  • Variable population size maintained population diversity, and ranking selection favored lower energy individuals.
  • The lowest energy achieved by GATS was superior to previous methods.

Conclusions:

  • The hybrid GATS algorithm leverages the strengths of both GA and TS.
  • It overcomes GA's limitations by incorporating TS's memory functions for better global optimization.
  • GATS effectively predicts 3D protein structures with enhanced performance.