Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Molecular Models

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.

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 Organization

Protein Organization

Protein Organization

Protein Organization

Molecular Shapes

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...

You might also read

Related Articles

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

Sort by

Same author

Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets.

bioRxiv : the preprint server for biology·2026

Same author

Systematic discovery of pro- and anti-HIV host factors in primary human CD4+ T cells.

Cell·2026

Same author

A Dose-Finding Design for Drug Combinations Using a Bayesian 4 Parameter Logistic Model With Penalised D-Optimality.

Pharmaceutical statistics·2026

Same author

The scientific legacy of Martin Karplus from the perspective of his collaborators.

Biophysical journal·2026

Same author

Phase 1 study of ceralasertib, an ATR kinase inhibitor, in combination with durvalumab in patients with recurrent or metastatic NSCLC or HNSCC.

British journal of cancer·2026

Same author

The filamentous ultrastructure of the PopZ condensate is required for its cellular function.

Nature structural & molecular biology·2026

Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 2, 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

Protein structure modeling with MODELLER.

Benjamin Webb¹, Andrej Sali

¹Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|February 28, 2014

Summary

This summary is machine-generated.

Computational protein structure modeling addresses the gap between vast genome data and limited experimental structures. MODELLER software can generate accurate protein models, aiding in the characterization of over half of known protein sequences.

More Related Videos

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

3D Printing of Biomolecular Models for Research and Pedagogy

3D Printing of Biomolecular Models for Research and Pedagogy

Published on: March 13, 2017

Related Experiment Videos

Last Updated: May 2, 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

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

3D Printing of Biomolecular Models for Research and Pedagogy

3D Printing of Biomolecular Models for Research and Pedagogy

Published on: March 13, 2017

Area of Science:

Structural bioinformatics
Computational biology
Genomics

Background:

Genome sequencing rapidly expands protein sequence data.
Experimental protein structure determination is experimentally intensive, yielding limited atomic-resolution structures.
A significant gap exists between known protein sequences and their experimentally determined structures.

Purpose of the Study:

To demonstrate the utility of computational protein structure modeling.
To illustrate the application of MODELLER for comparative protein modeling.
To assess the accuracy and applicability of automated modeling protocols.

Main Methods:

Utilizing MODELLER software for comparative protein structure modeling.
Developing and automating protocols for protein model construction.
Evaluating the accuracy of generated protein models.

Main Results:

Comparative models were successfully constructed for proteins with unknown structures.
Automated protocols yielded models of useful accuracy for a substantial portion of known protein sequences.
Over half of all known protein sequences could be modeled with useful accuracy.

Conclusions:

Computational protein structure modeling, exemplified by MODELLER, effectively bridges the sequence-structure gap.
Automated modeling protocols offer a scalable solution for characterizing large numbers of protein sequences.
This approach significantly enhances the potential for understanding protein function from sequence data.