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

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...

Stability of structures

Stability of structures

In mechanical engineering, the stability of systems under various forces is critical for designing durable and efficient structures. One fundamental way to explore these concepts is by analyzing systems like two rods connected at a pivot point, O, with a torsional spring of spring constant k at the pivot point. This system is similar in appearance to a scissor jack used to change tires on a car. In this case, the arms of the linkage (equivalent to the rods in this system) are entirely vertical,...

Mutations

Mutations

Structural Protein Function

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to...

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

Protein and Protein Structures

Protein and Protein Structures

You might also read

Related Articles

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

Sort by

Same author

OMAMA-DB: the Oregon-Massachusetts Mammography Database.

Journal of medical imaging (Bellingham, Wash.)·2026

Same author

How Functional Variants Reconfigure the Rac2 Conformational Landscape.

bioRxiv : the preprint server for biology·2026

Same author

Evaluation of CendR peptides mined from protein databases as potential inhibitors of neuropilin-1 using an in-silico molecular modeling approach.

Journal of molecular graphics & modelling·2026

Same author

Implementation strategies to integrate HIV and hypertension care in Kampala and Wakiso districts, Uganda: study protocol for a stepped wedge cluster randomized trial (PULESA-Uganda).

BMC health services research·2025

Same author

Economic Evaluation of the HEARTS Standardized Hypertension Treatment Program With Fixed-Dose Combination Pills in Chile Primary Care Clinics.

Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research·2025

Same author

Country-level impact of climate change on maternal and newborn health: Associations between temperature, precipitation, maternal mortality, stillbirth, and neonatal mortality in the Democratic Republic of the Congo.

Environment international·2025

Search research articles

Related Experiment Video

Updated: Feb 15, 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

Predicting the Effect of Single and Multiple Mutations on Protein Structural Stability.

Ramin Dehghanpoor¹, Evan Ricks², Katie Hursh³

¹Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA. ramin.dehghanpoor001@umb.edu.

Molecules (Basel, Switzerland)

|February 1, 2018

Summary

Predicting protein stability changes from mutations is crucial for drug design. This study uses machine learning and in silico methods to accurately forecast the impact of single and double point mutations on protein stability.

Keywords:

DNN RF SVR machine learning protein mutational study rigidity analysis

More Related Videos

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

Production of Disulfide-stabilized Transmembrane Peptide Complexes for Structural Studies

Production of Disulfide-stabilized Transmembrane Peptide Complexes for Structural Studies

Published on: March 6, 2013

Related Experiment Videos

Last Updated: Feb 15, 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

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

Production of Disulfide-stabilized Transmembrane Peptide Complexes for Structural Studies

Production of Disulfide-stabilized Transmembrane Peptide Complexes for Structural Studies

Published on: March 6, 2013

Area of Science:

Computational Biology
Protein Engineering
Bioinformatics

Background:

Predicting protein stability changes due to point mutations is vital for pharmaceutical drug design, particularly for diseases.
Experimental mutagenesis studies are time-consuming and costly, necessitating computational alternatives.
Computational methods offer a promising approach to complement wet-lab experiments in assessing mutation effects.

Purpose of the Study:

To compare and assess the utility of various machine learning methods for predicting the effects of single and double point mutations on protein stability.
To evaluate the accuracy of Support Vector Regression (SVR), Random Forest (RF), and Deep Neural Network (DNN) models in predicting mutation-induced stability changes.
To identify key features contributing to prediction accuracy and develop a consensus prediction model.

Main Methods:

In silico generation of mutant protein structures.
Computation of rigidity metrics as features for machine learning models.
Application of SVR, RF, and DNN models to predict stability changes.
Validation against experimental ΔΔG stability data.
Ablation studies and a voting scheme for model synthesis.

Main Results:

Machine learning models achieved high accuracy in predicting protein stability changes.
Pearson Correlation values reached 0.71 for single mutations and 0.81 for double mutations.
Ablation studies identified crucial features for prediction accuracy.
A voting scheme combining multiple models further improved prediction synthesis.

Conclusions:

Computational methods, particularly machine learning, are effective tools for predicting protein stability changes caused by mutations.
The developed in silico approach can significantly aid pharmaceutical drug design by prioritizing mutations for further study.
Accurate prediction of mutation effects on protein stability can accelerate the development of therapies for various diseases.