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

You might also read

Related Articles

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

Sort by
Same author

Electrolyte Engineering Enables Selective Electrocatalytic Hydrogenation of Furfural to 2-Methylfuran.

Journal of the American Chemical Society·2026
Same author

Correction to "Unraveling the Effects of Fe Incorporation on High-Performance Water-Splitting Photoanodes".

Journal of the American Chemical Society·2026
Same author

Catalytic Asymmetric Hydration of Alkenes.

Journal of the American Chemical Society·2026
Same author

Predicting Enantioselectivity via Kinetic Simulations on Gigantic Reaction Path Networks.

ACS central science·2026
Same author

Vibrational Quantum-State-Controlled Reactivity in the O<sub>2</sub><sup>+</sup> + C<sub>3</sub>H<sub>4</sub> Reaction.

The journal of physical chemistry letters·2026
Same author

Synergistic ruthenium single-atom and nanoparticles in nickel as cooperative catalysts for the alkaline hydrogen evolution reaction.

Nanoscale·2026

Related Experiment Video

Updated: Nov 1, 2025

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

5.2K

DockOnSurf: A Python Code for the High-Throughput Screening of Flexible Molecules Adsorbed on Surfaces.

Carles Martí1, Sarah Blanck2, Ruben Staub1

  • 1Univ Lyon, Ens de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F69342 Lyon, France.

Journal of Chemical Information and Modeling
|June 23, 2021
PubMed
Summary

DockOnSurf is a new open-source Python package that automates the discovery of molecule-surface adsorption configurations. It enables efficient, systematic, and traceable high-throughput screening for catalysis and nanoscience research.

More Related Videos

A Rapid and Quantitative Fluorimetric Method for Protein-Targeting Small Molecule Drug Screening
08:34

A Rapid and Quantitative Fluorimetric Method for Protein-Targeting Small Molecule Drug Screening

Published on: October 16, 2015

10.2K
Automated Two-dimensional Spatiotemporal Analysis of Mobile Single-molecule FRET Probes
08:26

Automated Two-dimensional Spatiotemporal Analysis of Mobile Single-molecule FRET Probes

Published on: November 23, 2021

2.8K

Related Experiment Videos

Last Updated: Nov 1, 2025

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

5.2K
A Rapid and Quantitative Fluorimetric Method for Protein-Targeting Small Molecule Drug Screening
08:34

A Rapid and Quantitative Fluorimetric Method for Protein-Targeting Small Molecule Drug Screening

Published on: October 16, 2015

10.2K
Automated Two-dimensional Spatiotemporal Analysis of Mobile Single-molecule FRET Probes
08:26

Automated Two-dimensional Spatiotemporal Analysis of Mobile Single-molecule FRET Probes

Published on: November 23, 2021

2.8K

Area of Science:

  • Computational chemistry
  • Materials science
  • Surface science

Background:

  • Understanding molecular adsorption on surfaces is crucial for catalysis, nanoscience, and tribology.
  • Existing methods for determining low-energy adsorption configurations can be computationally intensive and lack systematic exploration.
  • Handling polyfunctional and flexible molecules presents a significant challenge in adsorption studies.

Purpose of the Study:

  • To introduce DockOnSurf, an open-source Python package for automating the generation and optimization of molecular adsorption configurations.
  • To provide a high-throughput workflow for systematic, customizable, and traceable screening of adsorbate-surface interactions.
  • To facilitate the study of chemically relevant structures, including flexible molecules and proton dissociation.

Main Methods:

  • Development of an open-source Python package, DockOnSurf.
  • Implementation of a high-throughput screening strategy that divides configurational space into chemically meaningful domains.
  • Consideration of various adsorption parameters: molecular conformers, surface sites, anchoring points, orientations, and proton dissociation.
  • Demonstration using examples like CO on gold nanoparticles and sorbitol on hematite.

Main Results:

  • DockOnSurf automates the generation and optimization of low-energy adsorption configurations.
  • The package handles polyfunctional and flexible adsorbates effectively.
  • The screening strategy allows for systematic exploration of adsorbate-surface interactions.
  • Demonstrated performance across diverse examples, showcasing versatility.

Conclusions:

  • DockOnSurf enhances efficiency, traceability, and ease of use in surface science research.
  • The package aids in the discovery of optimal adsorbate-surface configurations for various applications.
  • It is a valuable tool for researchers in tribology, catalysis, nanoscience, and surface science.