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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

1.0K
1.0K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.1K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.1K
Protein Organization01:24

Protein Organization

7.2K
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....
7.2K
Molecular Models02:00

Molecular Models

37.5K
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.
37.5K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

28.0K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
28.0K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

19.9K
19.9K

You might also read

Related Articles

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

Sort by
Same author

Benchmark of Available Explicit Solvent Models in CHARMM36m to Characterize Glycosaminoglycans.

The journal of physical chemistry. B·2025
Same author

Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.

The journal of physical chemistry. B·2022
Same author

Elucidating the solution structure of the K-means cost function using energy landscape theory.

The Journal of chemical physics·2022
Same author

Improving double-ended transition state searches for soft-matter systems.

The Journal of chemical physics·2020
Same author

Mind the gap: testing the Rayleigh hypothesis in T-matrix calculations with adjacent spheroids.

Optics express·2019
Same author

Tunneling Splittings in Water Clusters from Path Integral Molecular Dynamics.

The journal of physical chemistry letters·2019

Related Experiment Video

Updated: May 4, 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

70.1K

Communication: a new paradigm for structure prediction in multicomponent systems.

D Schebarchov1, D J Wales1

  • 1University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

The Journal of Chemical Physics
|December 17, 2013
PubMed
Summary

We developed a new deterministic search scheme for optimizing multicomponent systems. This method significantly outperforms traditional global optimization techniques by efficiently exploring chemical ordering.

More Related Videos

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

9.3K
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

1.3K

Related Experiment Videos

Last Updated: May 4, 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

70.1K
Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

9.3K
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

1.3K

Area of Science:

  • Computational materials science
  • Chemical physics
  • Combinatorial optimization

Background:

  • Global optimization is crucial for determining the lowest energy structures of multicomponent systems.
  • Conventional methods like basin-hopping can be inefficient for exploring complex chemical ordering.
  • Understanding chemical arrangements is key to designing materials with desired properties.

Purpose of the Study:

  • To develop a more efficient global optimization strategy for multicomponent systems.
  • To investigate a deterministic search scheme inspired by graph partitioning.
  • To improve the exploration of chemical ordering in fixed-composition systems.

Main Methods:

  • A deterministic search scheme based on graph partitioning principles was devised.
  • The search is guided by energy gains (ΔEij, ΔEi) from particle permutations.
  • A self-guided basin-hopping variant was developed, weighting particles by approximate energy changes.
  • Geometry relaxation follows each permutation to relieve strain.

Main Results:

  • The deterministic search scheme demonstrated orders-of-magnitude improvement over conventional methods.
  • Energy gain calculations (ΔEij, ΔEi) provide unbiased guidance for the search.
  • The self-guided basin-hopping variant significantly improved optimization for segregated systems.
  • Approximation of ΔEi is efficient for site-separable force fields.

Conclusions:

  • A novel, highly efficient deterministic search method for multicomponent system optimization has been established.
  • The energy-guided approach offers a significant advancement over existing global optimization techniques.
  • This method provides a powerful tool for discovering optimal chemical ordering in materials science.