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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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...

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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

Comparative modeling of proteins.

Gerald H Lushington1

  • 1Molecular Graphics and Modeling Laboratory, University of Kansas, Lawrence, KS.

Methods in Molecular Biology (Clifton, N.J.)
|May 1, 2008
PubMed
Summary

Accurate in silico protein structure prediction is crucial for biological discovery. This chapter details comparative modeling strategies for reliable and efficient three-dimensional protein structure analysis.

Area of Science:

  • Biochemistry and structural biology
  • Computational biology and bioinformatics

Background:

  • Three-dimensional protein structure analysis drives biological and medical discovery.
  • Laboratory analysis of all proteins is infeasible, necessitating efficient in silico methods.
  • Comparative modeling is the leading technique for accurate protein structure prediction.

Purpose of the Study:

  • To focus on the philosophy and strategies for successful comparative modeling.
  • To provide guidance on achieving reliable and accurate protein structure models.
  • To discuss key aspects of the comparative modeling workflow.

Main Methods:

  • Template selection and sequence alignment
  • Spatial alignment and loop/gap modeling
  • Side chain modeling, structural refinement, and validation

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Last Updated: Jul 5, 2026

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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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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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07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Main Results:

  • Detailed strategies for template selection and sequence/spatial alignment.
  • Methods for accurate loop, gap, and side chain modeling.
  • Techniques for structural refinement and model validation.

Conclusions:

  • Comparative modeling offers an expeditious approach to protein structure prediction.
  • Successful implementation requires careful attention to specific modeling strategies.
  • Accurate in silico models are vital for understanding disease mechanisms and developing treatments.