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

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...
Conformations of Butane02:20

Conformations of Butane

Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are degenerate and have...
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...

You might also read

Related Articles

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

Sort by
Same author

Single-Stage Reverse High Tibial Osteotomy and Total Knee Arthroplasty for Valgus Extra-Articular Deformity After Failed HTO: A Matched-Pair Pilot Study.

Journal of clinical medicine·2026
Same author

Machine Learning Meets Pharmacokinetics: A Comparative Analysis of Predictive Models for Plasma Concentration-Time Profiles.

CPT: pharmacometrics & systems pharmacology·2026
Same author

Boron-Doping of a Macrocyclic Tetrafuran Framework Unveils an Expanded Porphyrinoid With Switchable (Anti)Aromaticity and Conformational Dynamics.

Angewandte Chemie (International ed. in English)·2026
Same author

A dihydrouracil CRBN ligand mitigates IMiD associated safety liabilities in heterobifunctional targeted protein degrader.

Nature communications·2026
Same author

Expanded Boraporphyrinoids: Boron Macrocycles with Redox Switchable Magnetic (Anti)aromaticity and Strong Near-Infrared Absorption.

Journal of the American Chemical Society·2026
Same author

The role of electron spin in molecular photochemical and photophysical processes: theory and experiment.

Physical chemistry chemical physics : PCCP·2025

Related Experiment Video

Updated: Jun 2, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Efficiency of tabu-search-based conformational search algorithms.

Christoph Grebner1, Johannes Becker, Svetlana Stepanenko

  • 1Julius-Maximilians-Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Am Hubland, 97074 Würzburg, Germany.

Journal of Computational Chemistry
|May 5, 2011
PubMed
Summary

This study compares molecular modeling methods for faster drug discovery. Combining basin hopping (BH) and gradient only tabu search (GOTS) significantly improves efficiency and speed for conformational searches.

Keywords:
Monte Carlo with minimizationTabu searchbasin hoppingconformational searchglobal optimizationsimulated annealing

More Related Videos

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Related Experiment Videos

Last Updated: Jun 2, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

Area of Science:

  • Computational chemistry and molecular modeling.
  • Drug discovery and development.
  • Bioinformatics and computational biology.

Background:

  • Efficient conformational search is crucial for molecular modeling.
  • Existing methods like molecular dynamics, simulated annealing, and basin hopping (BH) have limitations.
  • Gradient only tabu search (GOTS) is a previously suggested tabu-search-based approach.

Purpose of the Study:

  • To compare the efficiency of GOTS with established methods (molecular dynamics, simulated annealing, BH).
  • To evaluate the performance of a combined BH and GOTS approach.
  • To investigate the utility of hydrogen-bond-formed ring structures as starting points for conformational searches.

Main Methods:

  • Comparative analysis of molecular dynamics, simulated annealing, basin hopping (BH), and gradient only tabu search (GOTS).
  • Implementation and testing of a hybrid approach combining BH and GOTS.
  • Utilizing hydrogen-bond-formed ring structures as initial conformers.

Main Results:

  • The gradient only tabu search (GOTS) procedure demonstrates significant success.
  • The combined BH and GOTS approach outperforms individual methods in efficiency and speed.
  • Hydrogen-bond-formed ring structures are effective starting points for conformational investigations, particularly for peptides and organic ligands with biological activity.

Conclusions:

  • The hybrid basin hopping and gradient only tabu search method offers superior efficiency and speed for conformational searching.
  • Utilizing specific ring structures can enhance the conformational search process for biologically relevant molecules.
  • This research contributes to the development of faster and more reliable algorithms for molecular modeling and drug discovery.