Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Signal Sequences and Sorting Receptors01:41

Signal Sequences and Sorting Receptors

Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods with a Focus on FunFOLD3.

Methods in molecular biology (Clifton, N.J.)·2021
Same author

Methods for the Refinement of Protein Structure 3D Models.

International journal of molecular sciences·2019
Same author

Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures.

International journal of molecular sciences·2017
Same author

RAPIDSNPs: A new computational pipeline for rapidly identifying key genetic variants reveals previously unidentified SNPs that are significantly associated with individual platelet responses.

PloS one·2017
Same author

In silico Identification and Characterization of Protein-Ligand Binding Sites.

Methods in molecular biology (Clifton, N.J.)·2016
Same author

Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods.

International journal of molecular sciences·2015

Related Experiment Video

Updated: Jul 9, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Aligning sequences to structures.

Liam James McGuffin1

  • 1The University of Reading, Reading, UK.

Methods in Molecular Biology (Clifton, N.J.)
|December 14, 2007
PubMed
Summary

Template-based protein structure prediction methods are highly successful because most new proteins share structures with known ones. This chapter reviews these methods, from traditional to state-of-the-art, including structural annotation databases and practical guides.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • Most newly sequenced proteins adopt structures similar to experimentally determined ones.
  • Template-based methods are the most successful approaches for protein structure prediction.
  • These methods rely on aligning target sequences to known structures in a fold library.

Purpose of the Study:

  • To discuss the evolution of template-based protein fold prediction techniques.
  • To highlight recent advancements in structural annotation databases.
  • To provide a practical guide for sequence-to-structure alignment and discuss future directions.

Main Methods:

  • Review of traditional and state-of-the-art template-based protein structure prediction algorithms.

More Related Videos

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Related Experiment Videos

Last Updated: Jul 9, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

  • Discussion of structural annotation databases derived from proteome-wide sequence alignments.
  • Step-by-step guide for aligning target sequences to known protein structures.

    • Main Results:

    • Template-based methods have evolved significantly, offering powerful tools for predicting protein structures.
    • Structural annotation databases provide valuable resources for understanding protein folds across entire proteomes.
    • Practical alignment guides facilitate the application of these methods.

    Conclusions:

    • Template-based approaches remain a cornerstone of protein structure prediction due to the conservation of protein folds.
    • Advancements in databases and methodologies continue to enhance prediction accuracy and scope.
    • Future directions involve further refinement of alignment algorithms and database integration.