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

Small molecule recognition: solid angles surface representation and molecular shape complementarity.

R Norel1, H J Wolfson, R Nussinov

  • 1Computer Science Department, School of Mathematical Sciences, Tel Aviv University, Tel Aviv, 69978, Israel.

Combinatorial Chemistry & High Throughput Screening
|September 2, 1999
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

Speech-based characterization of dopamine replacement therapy in people with Parkinson's disease.

NPJ Parkinson's disease·2020
Same author

Mutations in LZTR1 drive human disease by dysregulating RAS ubiquitination.

Science (New York, N.Y.)·2018
Same author

Contribution of salt bridges toward protein thermostability.

Journal of biomolecular structure & dynamics·2012
Same author

GOSSIP: a method for fast and accurate global alignment of protein structures.

Bioinformatics (Oxford, England)·2011
Same author

Towards drugs targeting multiple proteins in a systems biology approach.

Current topics in medicinal chemistry·2007
Same author

MASS: multiple structural alignment by secondary structures.

Bioinformatics (Oxford, England)·2003
Same journal

Integrated Multi-Omics Identification of Novel Diagnostic Biomarkers and Immunometabolic Therapeutic Targets in Osteoporosis via Machine Learning.

Combinatorial chemistry & high throughput screening·2026
Same journal

Exploration and Prospects of Core Research Hotspots in the Mechanisms of Traditional Chinese Medicine for Treating Digestive System Malignancies Based on Bibliometrics.

Combinatorial chemistry & high throughput screening·2026
Same journal

Investigating the Potential Pharmacological Mechanisms of Huangqi in Allergic Rhinitis Using Network Pharmacology and Molecular Docking Strategies.

Combinatorial chemistry & high throughput screening·2026
Same journal

DNMT3A-driven Clonal Expansion of Hematopoiesis Influences Autoimmunity Mediated by Distinct Immune Cell Populations: A Mendelian Randomization Study.

Combinatorial chemistry & high throughput screening·2026
Same journal

UPLC-Q-TOF-MS/MS Combined with Network Pharmacology and Molecular Docking Revealed the Mechanism of Zhi Ke He Ji Oral Solution for the Treatment of Pneumonia.

Combinatorial chemistry & high throughput screening·2026
Same journal

Analysis of Chemical Components and Pharmacological Activities of Different Processing Methods in Magnolia denudata Desr. 'Hailuo' Using GC-MS and Network Pharmacology.

Combinatorial chemistry & high throughput screening·2026
See all related articles

This study shows that solid angle molecular surface representation and shape complementarity are effective for recognizing small molecules, like drugs, by their protein and DNA receptors. This method aids in efficiently scanning large drug databases for lead compounds.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Protein-protein recognition relies on shape complementarity.
  • The role of shape complementarity in small molecule-receptor recognition is less understood.
  • Solid angle molecular surface representation is effective for large protein matching.

Purpose of the Study:

  • To evaluate the solid angle molecular surface representation for small molecule-receptor fitting.
  • To determine the significance of shape complementarity in small molecule recognition.
  • To assess the applicability of these methods for large-scale drug screening.

Main Methods:

  • Docking of 185 receptor-small ligand molecule pairs.
  • Utilizing computer-vision based docking algorithms for efficiency.

Related Experiment Videos

  • Analysis of solid angle calculations and shape complementarity.

    • Main Results:

    • Solid angle representation performs adequately for small ligands.
    • Shape complementarity is a significant factor in small molecule-receptor recognition.
    • Efficient algorithms enable large-scale docking experiments in minutes.

    Conclusions:

    • Solid angle molecular surface representation is suitable for small molecule recognition.
    • Shape complementarity plays a crucial role in drug-receptor interactions.
    • Efficient computational methods accelerate the identification of potential drug candidates.