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 Experiment Videos

A geometry-based suite of molecular docking processes

D Fischer1, S L Lin, H L Wolfson

  • 1Computer Science Department, School of Mathematical Sciences, Tel Aviv University, Israel.

Journal of Molecular Biology
|April 28, 1995
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Time-resolved 3D momentum spectroscopy in continuous wave atomic photoionization experiments.

The Review of scientific instruments·2025
Same author

Genetic architecture and genomic prediction for yield, winter damage, and digestibility traits in timothy (Phleum pratense L.) using genotyping-by-sequencing data.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·2025
Same author

Incorporating the concept of overtransfusion into hemovigilance monitoring: An expert-based definition and criteria from the International HIT-OVER Forum.

Transfusion·2024
Same author

Microplastic-antifouling paint particle contamination alters microbial communities in surrounding marine sediment.

The Science of the total environment·2024
Same author

[Prehospital postcardiac-arrest-sedation and -care in the Federal Republic of Germany-a web-based survey of emergency physicians].

Medizinische Klinik, Intensivmedizin und Notfallmedizin·2023
Same author

Reaction microscope for investigating ionization dynamics of weakly bound alkali dimers.

The Review of scientific instruments·2022
Same journal

Biologically Relevant, Cationic Residues in Human Rhinovirus Stabilize Capsid-Bound RNA Duplexes, and Restrict Capsid Flexibility.

Journal of molecular biology·2026
Same journal

Cryo-EM structures of phage T4 infection intermediate.

Journal of molecular biology·2026
Same journal

A classic fold with a twist: Structural architecture of Dhillonvirus phage Bas18.

Journal of molecular biology·2026
Same journal

Tesorai Search: cloud-based database search engine boosts identifications for mass spectrometry proteomics with a pretrained peptide-spectrum deep-learning model.

Journal of molecular biology·2026
Same journal

Characterization of diverse functions of NRF1 nuclear localization sequence.

Journal of molecular biology·2026
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
See all related articles

We developed a geometry-based molecular docking suite for efficient and accurate protein-protein and protein-small molecule binding predictions. This computational tool enhances drug discovery by rapidly identifying high-quality molecular conformations.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Bioinformatics

Background:

  • Molecular docking is crucial for understanding biological interactions and drug discovery.
  • Existing methods can be computationally intensive and may lack accuracy.

Purpose of the Study:

  • To develop a novel, efficient, and accurate geometry-based computational suite for molecular docking.
  • To enable rapid prediction of protein-protein and protein-small molecule complexes.

Main Methods:

  • Developed a molecular surface representation using critical points and normals.
  • Implemented a docking algorithm based on the Geometric Hashing technique.
  • Utilized a three-layer scoring system for inter-penetration and contact filtering.

Related Experiment Videos

Main Results:

  • Achieved accurate and fast molecular docking for diverse complexes and unbound molecules.
  • Demonstrated high efficacy in a pipelined operation.
  • Validated geometrically docked conformations using energy evaluation (van der Waals and Coulombic potentials).

Conclusions:

  • The developed geometry-based suite offers a powerful tool for high-efficacy molecular docking.
  • This approach facilitates rapid and accurate prediction of molecular interactions.
  • The method shows promise for accelerating drug discovery and structural biology research.