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Related Concept Videos

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 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 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...
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 Folding01:22

Protein Folding

Overview

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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

Structure prediction of partial-length protein sequences.

Adrian Laurenzi1, Ling-Hong Hung, Ram Samudrala

  • 1Department of Computer Science & Engineering, University of Washington, Seattle, WA 98195-2350, USA. alaurenz@uw.edu

International Journal of Molecular Sciences
|July 23, 2013
PubMed
Summary

Top computational methods accurately predict partial protein structures from sequences over 50% complete. A confidence score aids in predicting protein "foldability" from limited sequence data, improving genome annotation.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Genomics

Background:

  • Protein structure is crucial for understanding protein function.
  • Current structure prediction methods are typically evaluated on full-length native protein sequences.
  • Limited sequence data, such as expressed sequence tags (ESTs), poses challenges for functional prediction.

Purpose of the Study:

  • To evaluate the accuracy of state-of-the-art protein structure prediction methods on partial protein sequences.
  • To explore the utility of structure prediction for inferring functions from partial sequences (e.g., ESTs).
  • To identify a reliable metric for assessing the foldability of arbitrary polypeptide sequences.

Main Methods:

  • Utilized top-performing computational protein structure prediction tools.
  • Tested prediction accuracy on sequences representing at least 50% of full-length proteins.
  • Developed and validated a confidence score for predicting sequence foldability.

Main Results:

  • Demonstrated that current top methods accurately predict partial protein structures from sequences comprising 50% or more of the full length.
  • Showcased the potential of structure prediction for functional annotation of partial sequences.
  • Identified a confidence score as a robust indicator of protein sequence foldability.

Conclusions:

  • Protein structure prediction methods are effective even with partial sequence information (>=50%).
  • Structure prediction and foldability assessment can enhance genome annotation, especially with limited or noisy sequence data.
  • This approach offers a valuable tool for analyzing expressed sequence tags and other partial sequences.