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

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.
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
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...
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

You might also read

Related Articles

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

Sort by
Same author

Expanding paclitaxel's therapeutic window: Investigating the pharmacokinetic, clinical formulation and mechanistic aspects of paclitaxel‑lipoate conjugate.

Oncology letters·2025
Same author

From Sequence to Solution: Intelligent Learning Engine Optimization in Drug Discovery and Protein Analysis.

Biotech (Basel (Switzerland))·2024
Same author

Alkyl Gallates as Potential Antibiofilm Agents: A Review.

Molecules (Basel, Switzerland)·2023
Same author

Inhibiting mutant KRAS G12D gene expression using novel peptide nucleic acid-based antisense: A potential new drug candidate for pancreatic cancer.

Oncology letters·2022
Same author

A Novel Docetaxel-Biotin Chemical Conjugate for Prostate Cancer Treatment.

Molecules (Basel, Switzerland)·2022
Same author

Forty-One Plant Extracts Screened for Dual Antidiabetic and Antioxidant Functions: Evaluating the Types of Correlation between -Amylase Inhibition and Free Radical Scavenging.

Molecules (Basel, Switzerland)·2021

Related Experiment Video

Updated: Jun 25, 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

New tips for structure prediction by comparative modeling.

Anwar Rayan1

  • 1QRC-Qasemi Research Center,Al-Qasemi Academic College, P.O.B. 124, Baka El-Garbiah 30100, Israel. a_rayan@qsm.ac.il

Bioinformation
|March 4, 2009
PubMed
Summary

Sequence identity does not reliably predict protein 3D structure model accuracy. Lower sequence identity in comparative modeling can surprisingly yield more accurate protein models, especially below 50%.

Keywords:
comparative modellinghomology modellingmodel refinement

More Related Videos

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

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

Related Experiment Videos

Last Updated: Jun 25, 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

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

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Comparative modeling predicts protein 3D structures using sequence alignment to known structures.
  • This technique is vital in biological research and drug discovery.
  • Model accuracy is often assumed to correlate with sequence identity between target and template proteins.

Purpose of the Study:

  • To investigate the relationship between sequence identity and the accuracy of comparative protein models.
  • To challenge the conventional assumption that higher sequence identity guarantees better model quality.

Main Methods:

  • Analysis of 4753 sequence and structure alignments.
  • Measurement of model accuracy using root mean square deviations (RMSD) of Calpha atoms between target and template structures.

Main Results:

  • Sequence identity is not a robust predictor of 3D model accuracy.
  • Lower sequence identity between target and template proteins frequently resulted in more accurate models.
  • This finding was observed across a large dataset.

Conclusions:

  • Rethink the reliance on sequence identity for assessing comparative model quality.
  • Develop new strategies to enhance comparative modeling, particularly for low sequence identity cases (<50%).
  • Improve protein structure prediction for challenging targets.