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Related Concept Videos

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.
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 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...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
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...

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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

The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending

Inbal Halperin1, Dariya S Glazer, Shirley Wu

  • 1Department of Genetics, 318 Campus Drive, Clark Center S240, Stanford, CA 94305, USA. inbal@helix.stanford.edu

BMC Genomics
|October 10, 2008
PubMed
Summary
This summary is machine-generated.

New protein structures from structural genomics often lack similarity to known proteins. The FEATURE framework enhances functional annotation by integrating structural and functional modeling, improving molecular function prediction.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Last Updated: Jun 29, 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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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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:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • Structural genomics yields novel protein structures lacking clear sequence or fold similarity to known proteins.
  • Traditional annotation methods struggle with these novel structures, necessitating advanced functional prediction techniques.

Purpose of the Study:

  • To provide an overview of the FEATURE framework for functional site recognition in macromolecular structures.
  • To detail recent advancements in the FEATURE framework for improved functional annotation.

Main Methods:

  • FEATURE framework for modeling and recognition of functional sites.
  • Automated training set selection for enhanced functional coverage.
  • Integration with molecular dynamics and loop modeling for improved performance.

Main Results:

  • FEATURE framework demonstrates flexibility in modeling functional sites.
  • Automated training set selection increases functional annotation coverage.
  • Coupling FEATURE with diversity generation methods enhances prediction accuracy.

Conclusions:

  • The FEATURE framework is a valuable tool for annotating molecular functions of novel protein structures.
  • Recent developments enhance FEATURE's utility in large-scale structural and functional modeling efforts.
  • Integrating structural and functional modeling is crucial for advancing structural genomics.