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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

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Genome Annotation and Assembly

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Nucleic Acid Structure01:25

Nucleic Acid Structure

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Updated: May 25, 2026

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

Methods for sequence-structure alignment.

Ceslovas Venclovas1

  • 1Institute of Biotechnology, Vilnius University, Vilnius, Lithuania. venclovas@ibt.lt

Methods in Molecular Biology (Clifton, N.J.)
|February 11, 2012
PubMed
Summary
This summary is machine-generated.

Homology modeling builds protein 3D structures using related sequences and templates. This guide details sequence-structure alignment methods, error detection, and optimization for accurate protein models.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Last Updated: May 25, 2026

The ITS2 Database
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Published on: March 12, 2012

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

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein modeling

Background:

  • Homology modeling leverages the principle that similar protein sequences fold into similar 3D structures.
  • Protein structure prediction relies on identifying homologous proteins with known 3D structures to serve as templates.
  • Accurate sequence-structure alignment is crucial for the reliability of homology models.

Purpose of the Study:

  • To provide an overview of sequence-structure alignment methods in homology modeling.
  • To discuss recent advancements enhancing alignment accuracy and performance.
  • To address the identification and correction of errors within alignment regions.

Main Methods:

  • Review of established and novel sequence-structure alignment algorithms.
  • Analysis of techniques for detecting and refining potentially erroneous alignment segments.
  • Guidance on utilizing available tools to optimize alignment quality.

Main Results:

  • Methodological developments have led to improved sequence-structure alignment performance.
  • Strategies for identifying and correcting alignment errors are presented.
  • Practical advice is offered for maximizing homology model accuracy through alignment optimization.

Conclusions:

  • Effective sequence-structure alignment is paramount for accurate homology modeling.
  • Continuous development of alignment methods and error-correction strategies is essential.
  • Users can enhance model quality by applying practical guidance for tool utilization.