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

Three-Dimensional Force System:Problem Solving01:30

Three-Dimensional Force System:Problem Solving

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...
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Three-Dimensional Force System01:30

Three-Dimensional Force System

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...
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...
Divergence Theorem in 3D Space01:20

Divergence Theorem in 3D Space

In vector calculus, flux measures the total flow of a vector field through a surface. For a closed surface in three-dimensional space, this means measuring how much of the field passes outward through every point on the boundary. Directly calculating this flux can be difficult when the surface has a complicated or irregular shape. The Divergence Theorem provides a powerful alternative by relating surface flux to behavior inside the enclosed region.The Divergence Theorem states that the outward...

You might also read

Related Articles

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

Sort by
Same author

Discovery of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 Main Protease through Computer-Aided Drug Design.

Journal of medicinal chemistry·2025
Same author

A case of pancreatic hamartoma with difficult preoperative diagnosis.

Clinical journal of gastroenterology·2025
Same author

Repurposing of the RIPK1-Selective Benzo[1,4]oxazepin-4-one Scaffold for the Development of a Type III LIMK1/2 Inhibitor.

ACS chemical biology·2025
Same author

Hilar Cholangiocarcinoma with Para-Aortic Lymph Node Metastasis Treated with Chemoimmunotherapy and Conversion Surgery: A Case Report.

Surgical case reports·2025
Same author

GLUT-1-negative Choroidal Malignant Melanoma with Liver Metastasis Recurrence 12 Years after Surgery without FDG Accumulation in a Recurrent Lesion on FDG-PET/CT.

Internal medicine (Tokyo, Japan)·2024
Same author

High-throughput screening of small-molecules libraries identified antibacterials against clinically relevant multidrug-resistant A. baumannii and K. pneumoniae.

EBioMedicine·2024

Related Experiment Video

Updated: Jun 23, 2026

Three-Dimensional Cephalometric Landmark Annotation Demonstration on Human Cone Beam Computed Tomography Scans
10:23

Three-Dimensional Cephalometric Landmark Annotation Demonstration on Human Cone Beam Computed Tomography Scans

Published on: September 8, 2023

Novel method for the evaluation of 3D conformation generators.

Terufumi Takagi1, Michiko Amano, Masaki Tomimoto

  • 1Pharmaceutical Research Division, Takeda Pharmaceutical Co., Ltd., Yodogawa-ku, Osaka 532-8686, Japan. takagi_terufumi@takeda.co.jp

Journal of Chemical Information and Modeling
|May 14, 2009
PubMed
Summary

A new method evaluates small molecule conformation generators by assessing their ability to reproduce bioactive conformation space, not just single conformations. This approach optimizes computational drug design by ensuring generated conformations accurately reflect real-world interactions.

More Related Videos

Clinical-oriented Three-dimensional Gait Analysis Method for Evaluating Gait Disorder
06:54

Clinical-oriented Three-dimensional Gait Analysis Method for Evaluating Gait Disorder

Published on: March 4, 2018

Related Experiment Videos

Last Updated: Jun 23, 2026

Three-Dimensional Cephalometric Landmark Annotation Demonstration on Human Cone Beam Computed Tomography Scans
10:23

Three-Dimensional Cephalometric Landmark Annotation Demonstration on Human Cone Beam Computed Tomography Scans

Published on: September 8, 2023

Clinical-oriented Three-dimensional Gait Analysis Method for Evaluating Gait Disorder
06:54

Clinical-oriented Three-dimensional Gait Analysis Method for Evaluating Gait Disorder

Published on: March 4, 2018

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Molecular modeling

Background:

  • Conformation generation is crucial for computer-aided drug design (CADD).
  • Current methods for evaluating conformation generators focus on reproducing single known bioactive conformations.
  • Limited availability of multiple experimental conformations per compound hinders comprehensive evaluation.

Purpose of the Study:

  • To develop a novel method for evaluating conformation generators.
  • To assess the ability of generators to reproduce the overall bioactive conformation space.
  • To determine optimal parameters for specific software (OMEGA) for better coverage and efficiency.

Main Methods:

  • Developed a novel evaluation method to measure performance against the entire bioactive conformation space.
  • Applied the method to evaluate OMEGA (OpenEye) conformation generator.
  • Identified optimal parameter sets for OMEGA balancing conformation space coverage and computational efficiency.

Main Results:

  • The novel evaluation method assesses the overall validity of generated conformations.
  • Increasing the number of generated conformations does not necessarily improve reproducibility of the bioactive conformation space.
  • Optimal parameters for OMEGA were identified, enhancing performance.

Conclusions:

  • The new evaluation method provides a more comprehensive assessment of conformation generators.
  • The findings suggest that focusing on the diversity and coverage of the bioactive conformation space is more important than simply increasing the number of generated conformations.
  • This method can guide the development and refinement of conformation generation algorithms and software.