Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
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...
4.3K
Protein Organization01:24

Protein Organization

6.7K
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....
6.7K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.6K
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...
12.6K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

11.0K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
11.0K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

3.8K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
3.8K
Ligand Binding Sites02:40

Ligand Binding Sites

13.0K
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...
13.0K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A Degron Decoy System Co-opts Pathological Seeding to Enable Clearance of Multimeric α-Synuclein.

bioRxiv : the preprint server for biology·2026
Same author

Augmented and Programmatically Optimized LLM Prompts Reduce Chemical Hallucinations.

Journal of chemical information and modeling·2025
Same author

Capturing the Conformational Heterogeneity of HSPB1 Chaperone Oligomers at Atomic Resolution.

Journal of the American Chemical Society·2025
Same author

GTExome: Modeling commonly expressed missense mutations in the human genome.

PloS one·2024
Same author

GTExome: Modeling commonly expressed missense mutations in the human genome.

bioRxiv : the preprint server for biology·2023
Same author

Biochemically prepared C-reactive protein conformational states differentially affect C1q binding.

BBA advances·2023

Related Experiment Video

Updated: Aug 9, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

195

Assessing protein homology models with docking reproducibility.

Alexander P Plonski1, Scott M Reed1

  • 1University of Colorado Denver, United States.

Journal of Molecular Graphics & Modelling
|February 22, 2023
PubMed
Summary

High-accuracy protein structure prediction is advancing, but side-chain precision is key for drug docking. Our study shows better backbone models improve small molecule binding site accuracy, especially with molecules having more rotatable bonds.

Keywords:
AlphaFoldArtificial intelligenceDockingHomology modeling

More Related Videos

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

68.8K
Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

438

Related Experiment Videos

Last Updated: Aug 9, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

195
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

68.8K
Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

438

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Drug Discovery

Background:

  • Recent advances in artificial intelligence, such as AlphaFold 2, have achieved high accuracy in predicting protein backbones.
  • Accurate protein structure prediction is crucial for applications like drug docking, which requires precise side-chain atom placement.
  • Homology models need validation for their utility in downstream applications.

Purpose of the Study:

  • To assess the reproducibility of small molecule binding to protein sites using homology models.
  • To investigate the correlation between protein backbone quality and small molecule docking accuracy.
  • To identify molecular features that enhance the detection of differences in binding sites between modeled and experimental structures.

Main Methods:

  • A library of 1334 small molecules was used for docking studies.
  • QuickVina-W, an optimized blind docking program, was employed.
  • The reproducibility of small molecule binding was examined against experimental and modeled protein structures.

Main Results:

  • Higher backbone quality in homology models led to greater similarity between small molecule docking results for experimental and modeled structures.
  • Specific subsets of the small molecule library were effective in distinguishing subtle differences in binding sites.
  • An increase in the number of rotatable bonds in small molecules correlated with more apparent differences in binding sites.

Conclusions:

  • Protein backbone quality significantly impacts the accuracy of small molecule docking predictions.
  • The choice of small molecules, particularly those with more rotatable bonds, can enhance the identification of structural variations in protein models.
  • These findings are critical for refining protein structure models for drug discovery and development.