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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 Organization01:13

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 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...

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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

GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction.

Hongyi Zhou1, Jeffrey Skolnick

  • 1Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA.

Biophysical Journal
|October 19, 2011
PubMed
Summary

A new scoring function, the generalized orientation-dependent all-atom potential (GOAP), significantly improves protein structure prediction accuracy. GOAP outperforms existing methods, especially for challenging homology-modeled and ab initio decoy sets.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Accurate scoring functions are crucial for protein structure prediction.
  • Existing methods often struggle with specific types of decoy sets.

Purpose of the Study:

  • To develop a novel, generalized orientation and distance-dependent all-atom statistical potential for protein structure prediction.
  • To improve the accuracy and reliability of scoring functions in computational protein modeling.

Main Methods:

  • Developed the generalized orientation-dependent all-atom potential (GOAP), incorporating relative orientation of heavy atom planes.
  • Decomposed GOAP into distance- and angle-dependent contributions, utilizing the DFIRE reference state.
  • Tested GOAP on 11 decoy sets (278 targets), comparing its performance against DFIRE, RWplus, and OPUS-PSP.

Main Results:

  • GOAP identified 226 native structures as the best among decoys, significantly outperforming DFIRE (127 targets).
  • GOAP showed major improvements on homology-modeled structures close to native and ROSETTA ab initio decoys.
  • GOAP outperformed OPUS-PSP by approximately 15% on these challenging decoy sets.

Conclusions:

  • GOAP represents a promising advancement in knowledge-based, all-atom statistical potentials for protein structure prediction.
  • The generalized orientation-dependent approach enhances scoring function performance, particularly for difficult prediction cases.
  • GOAP is available for download, facilitating further research and application in structural biology.