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

Two-Dimensional Force System01:20

Two-Dimensional Force System

869
A two-dimensional system in mechanical engineering involves the analysis of motion and forces in a plane. A two-dimensional force vector can be resolved into its components as:
869
Three-Dimensional Force System01:30

Three-Dimensional Force System

2.0K
In mechanical engineering, a three-dimensional force system is a system of forces acting in three dimensions, with forces applied along the x, y, and z coordinate axes. The three-dimensional force system is an important concept in mechanical engineering, as it allows engineers to understand and analyze the behavior of objects and structures in three dimensions. By understanding the forces acting on a system, engineers can design more efficient and effective mechanical systems that can withstand...
2.0K
Protein Folding01:22

Protein Folding

117.1K
Overview
117.1K
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

12.5K
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
12.5K
Intermolecular Forces03:13

Intermolecular Forces

57.5K
Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen...
57.5K
Three-Dimensional Force System:Problem Solving01:30

Three-Dimensional Force System:Problem Solving

619
A three-dimensional force system refers to a scenario in which three forces act simultaneously in three different directions. This type of problem is commonly encountered in physics and engineering, where it is necessary to calculate the resultant force on the system, which can then be used to predict or analyze the behavior of the object or structure under consideration.
To solve a three-dimensional force system, first resolve each force into its respective scalar components. Do this using...
619

You might also read

Related Articles

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

Sort by
Same author

Proteomic profiling of whole tissue sections in cardiac ATTR amyloidosis reveals increased extracellular matrix remodeling.

Cardiovascular pathology : the official journal of the Society for Cardiovascular Pathology·2026
Same author

Integrated omics reveal a unique antibacterial mechanism of action for the small molecule HSI#6.

Current research in microbial sciences·2026
Same author

Confirmation of monotypic immunofluorescence staining by mass spectrometry in a case of proliferative glomerulonephritis.

Histopathology·2026
Same author

FoldDelay web server: an online tool to quantify translation-driven delays in protein native contact formation.

Nucleic acids research·2026
Same author

Belgian recommendations for tissue diagnosis of amyloidosis.

Acta clinica Belgica·2026
Same author

Atomic structures of medin and Aβ fibrils reveal polymorphic remodeling in mixed amyloid systems.

Nature communications·2026

Related Experiment Video

Updated: May 29, 2025

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.1K

FoldX force field revisited, an improved version.

Javier Delgado1, Raul Reche1, Damiano Cianferoni1

  • 1Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.

Bioinformatics (Oxford, England)
|February 6, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces an updated FoldX force field, enhancing protein stability predictions with a larger, curated dataset and improved interaction parameters. The new version shows statistically significant improvements in predicting mutation effects on protein stability.

More Related Videos

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

12.7K
Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene
08:44

Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene

Published on: August 22, 2017

7.7K

Related Experiment Videos

Last Updated: May 29, 2025

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.1K
Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

12.7K
Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene
08:44

Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene

Published on: August 22, 2017

7.7K

Area of Science:

  • Computational Biology
  • Protein Engineering
  • Biophysics

Background:

  • The FoldX force field, initially validated on a smaller dataset, required updates due to advancements in high-resolution structural data.
  • A manually curated database of 5556 mutants (FoldX Stability Dataset - FSD) was created from high-confidence mutations in non-redundant X-ray structures (<2.5 Å resolution).

Purpose of the Study:

  • To develop an improved version of the FoldX force field by incorporating new interaction parameters and a larger, high-quality dataset.
  • To enhance the accuracy of predicting protein stability changes upon mutation.

Main Methods:

  • Curated a dataset of 2484 high-confidence mutations (FSD) from 5556 analyzed mutants.
  • Incorporated new parameters for pi stacking, pH dependency, aromatic-aromatic interactions, N-terminal capping, alpha-helix dipoles, methionine side-chain entropy, hydrogen bonds, and tryptophan solvation.
  • Validated the updated force field using the Validation FoldX Stability Dataset (VFSD).

Main Results:

  • The updated FoldX force field demonstrated significant improvements in predicting mutations, particularly those involving updated residues and interactions.
  • Performance on the VFSD dataset improved, with the correlation coefficient (R) increasing from 0.693 to 0.706 and RMSE decreasing from 1.277 to 1.252 kcal/mol.
  • Achieved 95% accuracy with a prediction error of ±0.85 kcal/mol and an AUC of 0.78 for predicting the sign of stability change.

Conclusions:

  • The revised FoldX force field offers enhanced accuracy for predicting protein stability changes.
  • The updated model provides a more reliable tool for protein engineering and biophysical studies.