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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.
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...
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...
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 Folding01:22

Protein Folding

Overview

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Related Experiment Video

Updated: Jun 2, 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

Accuracy of functional surfaces on comparatively modeled protein structures.

Jieling Zhao1, Joe Dundas, Sema Kachalo

  • 1Department of Bioengineering, University of Illinois at Chicago, 851 S. Morgan Street, Room 218, MC-063, Chicago, IL 60607, USA. jzhao31@uic.edu

Journal of Structural and Functional Genomics
|May 5, 2011
PubMed
Summary

Comparative modeling accurately predicts protein binding surfaces when sequence identity exceeds 45%. This method captures key functional atoms, aiding protein function prediction and drug design.

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Related Experiment Videos

Last Updated: Jun 2, 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

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Area of Science:

  • Structural Biology
  • Computational Biology
  • Biochemistry

Background:

  • Accurate protein functional surface identification is crucial for predicting protein function, enzyme mechanisms, and drug discovery.
  • The disparity between rapidly accumulating protein sequence data and available structural data necessitates robust methods for modeling functional surfaces from sequences.
  • Comparative modeling using known structural templates offers a promising approach to address this data gap.

Purpose of the Study:

  • To evaluate the accuracy of comparative modeling in reproducing protein binding surfaces.
  • To assess the reliability of computational models for identifying key elements of functional protein surfaces.

Main Methods:

  • Systematic construction of three-dimensional comparative models for 26,590 enzyme proteins using MODELLER.
  • Application of an alpha shape-based algorithm to identify and analyze pockets on modeled structures.
  • Large-scale computation of similarity metrics, including pocket Root Mean Square Deviation (RMSD) and fraction of functional atoms captured.

Main Results:

  • Modeled protein surfaces achieve an average RMSD of 0.5 Å when sequence identity to the template exceeds 45%.
  • These models capture 48% or more of the binding surface atoms, including nearly all critical atoms within binding pocket signatures.
  • The approach demonstrates high fidelity in reproducing the essential features of functional protein surfaces.

Conclusions:

  • Comparative modeling is a reliable strategy for accurately modeling protein functional and binding surfaces, especially when template sequence identity is high.
  • This method effectively identifies key atoms and structural features of binding pockets, supporting downstream applications in functional prediction and molecular docking.
  • The findings validate the utility of sequence-based modeling for understanding protein function in the era of big data.