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Protein Organization

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 Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
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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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Updated: Jun 23, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit

Yelena A Arnautova¹, Yury N Vorobjev, Jorge A Vila

¹Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca New York 14853-1301, USA.

|April 23, 2009

Summary

This summary is machine-generated.

New scoring functions for protein structure prediction show improved accuracy. The ECEPP05/SA model successfully ranks native-like protein structures, outperforming previous methods and enhancing theoretical structure refinement.

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Area of Science:

Computational Biology
Structural Bioinformatics
Biophysics

Background:

Accurate energy functions are vital for predicting protein structures and refining low-resolution models.
Distinguishing native-like protein conformations from non-native ones is a key challenge in computational structural biology.

Purpose of the Study:

To benchmark and compare the performance of novel scoring functions for protein structure prediction.
To evaluate scoring functions based on ECEPP/3 and ECEPP05 force fields with different implicit solvent models.

Main Methods:

Tested three scoring functions: ECEPP05/SA, ECEPP3/OONS, and ECEPP05/FAMBEpH.
Employed Monte Carlo-with-Minimization (MCM) simulations and direct energy calculations for scoring.
Evaluated performance by assessing the ability to rank native-like structures among protein decoys.

Main Results:

The ECEPP05/SA scoring function significantly improved native structure ranking compared to ECEPP3/OONS.
ECEPP05/SA ranked native-like structures within 3.5 Å Cα-RMSD as lowest energy for 76% of proteins.
The ECEPP05/FAMBEpH model further enhanced discrimination, achieving 89% accuracy.

Conclusions:

The ECEPP05/SA scoring function represents a substantial advancement in protein structure prediction accuracy.
The FAMBEpH solvation model offers improved discrimination by better describing protein-solvent interactions.
Future developments should consider protein-protein interactions to address limitations in discrimination.