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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.
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...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
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...
Protein and Protein Structures02:15

Protein and Protein Structures

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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Updated: Jun 1, 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

NCACO-score: an effective main-chain dependent scoring function for structure modeling.

Liqing Tian1, Aiping Wu, Yang Cao

  • 1National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

BMC Bioinformatics
|May 27, 2011
PubMed
Summary
This summary is machine-generated.

A new knowledge-based scoring function, NCACO-score, effectively models protein structures using a coarse-grained approach. This method accurately identifies native protein conformations and aids in predicting complex protein structures with speed and precision.

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Last Updated: Jun 1, 2026

A Protocol for Computer-Based Protein Structure and 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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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Biophysics

Background:

  • Effective scoring functions are crucial for accurate protein structure modeling.
  • Developing scoring functions that balance accuracy and speed remains a significant challenge in the field.
  • Previous efforts have focused on various approaches to scoring function development.

Purpose of the Study:

  • To develop a novel knowledge-based scoring function for rapid protein structure modeling.
  • To integrate diverse structural information into a scoring function based on a coarse-grained model.
  • To enhance the accuracy and speed of protein structure prediction.

Main Methods:

  • Developed NCACO-score, a knowledge-based scoring function utilizing a coarse-grained representation (N, Cα, C, O main-chain atoms).
  • Integrated various structural information within the NCACO-score framework.
  • Tested NCACO-score on the Decoys'R'Us datasets for native conformer recognition.
  • Applied NCACO-score to guide fragment assembly in protein structure prediction for CASP8 targets.

Main Results:

  • NCACO-score demonstrated high accuracy in distinguishing native protein conformers from decoys.
  • The scoring function effectively guided fragment assembly for protein structure prediction.
  • Achieved good performance in terms of both accuracy and speed for predicting structures of challenging targets (CASP8).

Conclusions:

  • NCACO-score, despite its coarse-grained basis, achieves high accuracy in discriminating native from decoy conformers.
  • NCACO-score is a highly effective tool for protein structure modeling.
  • The developed scoring function offers a promising balance of accuracy and speed for computational protein structure prediction.