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 Complex Assembly02:41

Protein Complex Assembly

16.7K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
16.7K
Protein Complex Assembly02:41

Protein Complex Assembly

2.5K
2.5K
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

6.5K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
6.5K
Assembly of Complex Microtubule Structures01:32

Assembly of Complex Microtubule Structures

2.4K
Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.
2.4K
Formation of Complex Ions03:45

Formation of Complex Ions

25.8K
A type of Lewis acid-base chemistry involves the formation of a complex ion (or a coordination complex) comprising a central atom, typically a transition metal cation, surrounded by ions or molecules called ligands. These ligands can be neutral molecules like H2O or NH3, or ions such as CN− or OH−. Often, the ligands act as Lewis bases, donating a pair of electrons to the central atom. These types of Lewis acid-base reactions are examples of a broad subdiscipline called coordination...
25.8K
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

30.7K
Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
30.7K

You might also read

Related Articles

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

Sort by
Same author

Understanding the physical processes behind DNA-DNA proximity ligation assays.

Research square·2025
Same author

Data-driven parametrization of molecular mechanics force fields for expansive chemical space coverage.

Chemical science·2025
Same author

RACER-m leverages structural features for sparse T cell specificity prediction.

Science advances·2024
Same author

Driving technology factors of carbon emissions: Theoretical framework and its policy implications for China.

The Science of the total environment·2023
Same author

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.

Nature communications·2023
Same author

Precise Steric Features Control Aminoacyl-tRNA Accommodation on the Ribosome.

The journal of physical chemistry. B·2022
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

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

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

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

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

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

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

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

Characterization of Bioactive Saponins from Sea Cucumbers.

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

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Jan 21, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
07:26

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

13.4K

Using SMOG 2 to Simulate Complex Biomolecular Assemblies.

Mariana Levi1, Prasad Bandarkar1, Huan Yang1

  • 1Department of Physics, Northeastern University, Boston, MA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|August 10, 2019
PubMed
Summary
This summary is machine-generated.

Structure-based (Gō-like) models simulate molecular assemblies. The SMOG 2 software package offers a versatile platform for designing and implementing these models, enabling detailed analysis of complex biological systems like the ribosome.

Keywords:
Coarse-grained modelsGō-modelProtein foldingSMOGStructure-based model

More Related Videos

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

3.1K
Assembly and Characterization of Biomolecular Memristors Consisting of Ion Channel-doped Lipid Membranes
08:07

Assembly and Characterization of Biomolecular Memristors Consisting of Ion Channel-doped Lipid Membranes

Published on: March 9, 2019

8.3K

Related Experiment Videos

Last Updated: Jan 21, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
07:26

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

Published on: November 21, 2013

13.4K
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

3.1K
Assembly and Characterization of Biomolecular Memristors Consisting of Ion Channel-doped Lipid Membranes
08:07

Assembly and Characterization of Biomolecular Memristors Consisting of Ion Channel-doped Lipid Membranes

Published on: March 9, 2019

8.3K

Area of Science:

  • Computational biology
  • Biophysics
  • Structural biology

Background:

  • Structure-based (Gō-like) models are widely used in computational biophysics.
  • These models utilize experimentally determined conformations to define energetic interactions.
  • Applications range from protein folding to large molecular assemblies.

Purpose of the Study:

  • To introduce the SMOG 2 software package, a versatile computational platform.
  • To provide an easy-to-use interface for designing and implementing structure-based models.
  • To facilitate the study of large-scale molecular assemblies.

Main Methods:

  • SMOG 2 utilizes XML-formatted files for user-defined model parameters.
  • The software maps interactions onto structures provided in PDB format.
  • Generated force field files are compatible with popular molecular dynamics suites.

Main Results:

  • SMOG 2 offers full user control over model parameters.
  • The package enables the definition of new structure-based models.
  • It supports the simulation of complex molecular assemblies.

Conclusions:

  • SMOG 2 is a powerful tool for structure-based modeling.
  • It simplifies the implementation of coarse-grained and all-atom models.
  • The software aids in the investigation of large biological systems, such as the ribosome.