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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 Organization01:24

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 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...
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...

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Related Experiment Video

Updated: Jun 22, 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

SAM-T08, HMM-based protein structure prediction.

Kevin Karplus1

  • 1Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA. karplus@soe.ucsc.edu

Nucleic Acids Research
|June 2, 2009
PubMed
Summary
This summary is machine-generated.

The SAM-T08 web server offers advanced protein structure prediction and valuable intermediate data. It demonstrated strong performance in the CASP8 assessment for various prediction types.

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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Bioinformatics tools

Background:

  • Protein structure prediction is crucial for understanding biological function.
  • Accurate prediction of three-dimensional protein structures remains a significant challenge in bioinformatics.
  • Web servers provide accessible platforms for computational biology research.

Purpose of the Study:

  • To introduce the SAM-T08 web server for protein structure prediction.
  • To highlight the diverse intermediate results provided by the server.
  • To report on the performance evaluation of SAM-T08 in a large-scale assessment.

Main Methods:

  • Utilizing iterative search procedures for multiple sequence alignments.
  • Predicting local structure features, including backbone properties and residue burial.
  • Employing calibrated E-values for assessing template search significance.
  • Generating residue-residue contact predictions.

Main Results:

  • The SAM-T08 server provides predicted 3D structures along with multiple sequence alignments.
  • It offers predictions of local structure features and residue-residue contacts.
  • The server achieved good performance across all prediction classes in the CASP8 assessment.

Conclusions:

  • SAM-T08 is a valuable web server for protein structure prediction.
  • The server's comprehensive output, including intermediate data, aids structural bioinformatics research.
  • Validated performance in CASP8 indicates its utility and reliability for the scientific community.