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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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 Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to

Ciro Leonardo Pierri1, Giovanni Parisi, Vito Porcelli

  • 1Department of Pharmaco-Biology, Laboratory of Biochemistry and Molecular Biology, University of Bari, Va E. Orabona, 4 - 70125 Bari, Italy. ciroleopierri@gmail.com

Biochimica Et Biophysica Acta
|May 4, 2010
PubMed
Summary
This summary is machine-generated.

Computational approaches aid in predicting protein function. This review details methods like comparative modeling and virtual screening for protein-ligand interactions, accelerating biochemical and medical research.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Protein functional characterization is crucial yet challenging in biochemical, medical, and computational sciences.
  • Computational methods can predict protein function, guiding experimental validation.
  • Comparative modeling requires homologous crystal structures for accurate 3D protein models.

Purpose of the Study:

  • To review the state-of-the-art computational approaches for 3D protein comparative modeling.
  • To explore computational strategies for studying protein-ligand interactions.
  • To present a combined strategy for protein function prediction using computational tools.

Main Methods:

  • Comparative modeling for constructing 3D protein structures.
  • Binding site prediction using various data sources.
  • Ligand docking and structure-based virtual screening of chemical libraries.
  • Multiple sequence alignment analysis.

Main Results:

  • Accurate 3D protein models can be built using comparative modeling when homologous structures are available.
  • Binding regions can be identified through predictors and analysis of homologous structures.
  • Virtual screening identifies potential chemical ligands for protein targets.
  • A multi-step strategy integrating these methods enhances protein function prediction.

Conclusions:

  • Computational approaches, including comparative modeling and virtual screening, are vital for predicting protein function.
  • Integrating multiple computational techniques offers a powerful strategy for protein characterization.
  • These methods accelerate discovery in biochemical and medical research by guiding experimental efforts.