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 Video

Updated: Jun 6, 2026

Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics
13:30

Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics

Published on: February 18, 2022

Fast surface-based travel depth estimation algorithm for macromolecule surface shape description.

Joachim Giard1, Patrice Rondao Alface, Jean-Luc Gala

  • 1Communications and Remote Sensing Laboratory, Université catholique de Louvain, Place du Levant, 2 (TELE), 1348 Louvain-la-neuve, Belgium. joachim.giard@uclouvain.be

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|November 13, 2010
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

Towards a Strengthened Addictions Neuroclinical Assessment (ANA) Framework: A Perspective on Current Assessment Approaches and The Added Value of Recovery-Inspired Dimensions.

Journal of studies on alcohol and drugs·2026
Same author

Exploring Hydroxytyrosol as a Promising Virucidal Agent: In Silico and In Vitro Insights into Enveloped Viruses.

Current issues in molecular biology·2026
Same author

Multi-Patient Vision Transformer for Markerless Tumor Motion Forecasting.

Biomedicines·2026
Same author

Machine learning-based combination of the central vein sign, cortical lesions and paramagnetic rim lesions: a web-based tool for the diagnosis of multiple sclerosis.

Brain communications·2026
Same author

Analytical Performance of Nanobody-Based Immunoassay and Immunosensing Platforms for Bacteria and Toxin Detection: A Systematic Review.

Antibodies (Basel, Switzerland)·2026
Same author

White matter microstructure alterations from alcohol use disorder persist into early abstinence.

Brain communications·2026
Same journal

circ2DGNN: circRNA-Disease Association Prediction via Transformer-Based Graph Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Hierarchical Hypergraph Learning in Association- Weighted Heterogeneous Network for miRNA- Disease Association Identification.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Discriminative Domain Adaption Network for Simultaneously Removing Batch Effects and Annotating Cell Types in Single-Cell RNA-Seq.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

MLW-BFECF: A Multi-Weighted Dynamic Cascade Forest Based on Bilinear Feature Extraction for Predicting the Stage of Kidney Renal Clear Cell Carcinoma on Multi-Modal Gene Data.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

An End-to-End Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction.

IEEE/ACM transactions on computational biology and bioinformatics·2024
Same journal

Generative Biomedical Event Extraction With Constrained Decoding Strategy.

IEEE/ACM transactions on computational biology and bioinformatics·2024
See all related articles

This study introduces a faster method for calculating Travel Depth, a measure of molecular shape. The new surface-based algorithm significantly reduces computation time for analyzing large molecules.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Molecular modeling

Background:

  • Travel Depth quantifies molecular shape, crucial for understanding active/binding sites.
  • Current methods use volume sampling and Dijkstra's algorithm, leading to high computational cost.
  • Existing algorithms are inefficient for large macromolecules due to unnecessary data processing.

Purpose of the Study:

  • To develop a more efficient algorithm for estimating Travel Depth.
  • To reduce the computational complexity of molecular shape analysis.
  • To enable high-resolution analysis of large macromolecule surfaces.

Main Methods:

  • A novel surface-based approach focusing on the Solvent-Excluded Surface (SES).
  • Eliminates the need for volume sampling, processing only relevant surface data.

More Related Videos

Application of High-speed Super-resolution SPEED Microscopy in Live Primary Cilium
07:53

Application of High-speed Super-resolution SPEED Microscopy in Live Primary Cilium

Published on: January 16, 2018

Related Experiment Videos

Last Updated: Jun 6, 2026

Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics
13:30

Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics

Published on: February 18, 2022

Application of High-speed Super-resolution SPEED Microscopy in Live Primary Cilium
07:53

Application of High-speed Super-resolution SPEED Microscopy in Live Primary Cilium

Published on: January 16, 2018

  • Utilizes Dijkstra's shortest path algorithm on the SES.

    • Main Results:

    • The proposed algorithm significantly reduces computational complexity.
    • Accurate Travel Depth estimations are achieved with considerably reduced processing times.
    • Enables high-resolution shape description for large macromolecules.

    Conclusions:

    • The surface-based method offers a substantial improvement over existing volume-based approaches.
    • This advancement facilitates more efficient and detailed analysis of molecular surface shapes.
    • The algorithm is particularly beneficial for studying large biomolecules.