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

Exploring fragment spaces under multiple physicochemical constraints.

Juri Pärn1, Jörg Degen, Matthias Rarey

  • 1Center for Bioinformatics, Hamburg, Germany. rarey@zbh.uni-hamburg.de

Journal of Computer-Aided Molecular Design
|June 29, 2007
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

PegaPlus─Interactive Machine Learning by Human Observation for Efficient Clustering and Analysis of Structure-Activity Data.

Journal of chemical information and modeling·2026
Same author

Enabling Automatic Generation of Protein-Ligand Complex Data Sets with Atomistic Detail.

Journal of chemical information and modeling·2026
Same author

Guiding Similarity Search in Chemical Fragment Spaces with Weighted Fingerprints.

Journal of chemical information and modeling·2026
Same author

ActivityFinder: Toward the Fully Automatic Integration of Structural and Binding Affinity Data.

Journal of chemical information and modeling·2026
Same author

A bottom-up approach to find lead compounds in expansive chemical spaces.

Communications chemistry·2025
Same author

Correction: SAVI Space-combinatorial encoding of the billion-size synthetically accessible virtual inventory.

Scientific data·2025
Same journal

A linear models approach to optimize carbazole-based dyes for solar cell applications.

Journal of computer-aided molecular design·2026
Same journal

DOCKweb: a web-based GUI platform for molecular modeling with DOCK6.

Journal of computer-aided molecular design·2026
Same journal

Two faces of drug repurposing data in machine learning-driven structure-based virtual screening supported by interaction fingerprints.

Journal of computer-aided molecular design·2026
Same journal

Repurposing bleomycin against Acinetobacter baumannii HisG: computational, biophysical, and antibacterial evidence.

Journal of computer-aided molecular design·2026
Same journal

Topological data analysis for antibody-drug conjugate payload discovery: a computational framework for mechanistic classification and target validation.

Journal of computer-aided molecular design·2026
Same journal

Commentary on the fundamentals and development of artificial intelligence models in the life sciences and best research practices.

Journal of computer-aided molecular design·2026
See all related articles

This study introduces a novel algorithm for enumerating chemical fragment spaces, enabling the generation of molecules with specific physicochemical properties. The method efficiently explores vast chemical possibilities, aiding drug discovery and molecular design.

Area of Science:

  • Computational Chemistry
  • Cheminformatics
  • Drug Discovery

Background:

  • Fragment spaces offer a way to represent vast numbers of potential molecules.
  • Enumerating these spaces is challenging due to their infinite nature.
  • Constrained enumeration is needed to generate molecules with desired properties.

Purpose of the Study:

  • To develop a new algorithm for enumerating chemical fragment spaces under specific constraints.
  • To enable the generation of molecules that adhere to predefined physicochemical profiles.
  • To improve the efficiency of exploring chemical diversity.

Main Methods:

  • Developed an algorithm for constrained enumeration of molecular fragment spaces.
  • Utilized min-max ranges of physicochemical properties to guide fragment selection.

Related Experiment Videos

  • Implemented a topology-based fragment filter to avoid redundant combinations.
  • Applied the algorithm to 40 target classes, generating tailored fragment spaces.

    • Main Results:

    • The algorithm successfully enumerated molecules obeying specified physicochemical properties.
    • The constrained approach significantly speeds up the calculation process.
    • Target-specific fragment spaces were characterized, and complete chemical subspaces were enumerated for most targets.
    • The method demonstrated applicability across diverse target classes.

    Conclusions:

    • The presented algorithm provides an efficient method for exploring and enumerating constrained chemical fragment spaces.
    • This approach facilitates the generation of targeted molecular libraries with desired properties.
    • The algorithm has significant potential for accelerating drug discovery and materials science research.